I know I missed a bunch in this thread, but here are some problems associated with the ark being real. They are taken from a variety of sources and are not my own words.
Wood is not the best material for shipbuilding. It is not enough that a ship be built to hold together; it must also be sturdy enough that the changing stresses don't open gaps in its hull. Wood is simply not strong enough to prevent separation between the joints, especially in the heavy seas that the Ark would have encountered. The longest wooden ships in modern seas are about 300 feet, and these require reinforcing with iron straps and leak so badly they must be constantly pumped. The ark was 450 feet long [ Gen. 6:15]. Could an ark that size be made seaworthy?
If the animals traveled from other parts of the world, many of them would have faced extreme difficulties. Some, like sloths and penguins, can't travel overland very well at all. Some, like koalas and many insects, require a special diet. How did they bring it along? Other animals are strict carnivores, and some of those specialize on certain kinds of foods, such as small mammals, insects, fish, or aquatic invertebrates. How did Noah determine and provide for all those special diets?
Getting all the animals aboard the Ark presents logistical problems which, while not impossible, are highly impractical. Noah had only seven days to load the Ark ( Gen. 7:4-10). If only 15764 animals were aboard the Ark (see section 3), one animal must have been loaded every 38 seconds, without letup. Since there were likely more animals to load, the time pressures would have been even worse.
According to the Bible, Noah took samples of all animals alive at the time of the Flood. If, as creationists claim, all fossil-bearing strata were deposited by the Flood, then all the animals which became fossils were alive then. Therefore all extinct land animals had representatives aboard the ark. It is also worth pointing out that the number of extinct species is undoubtedly greater than the number of known extinct species. New genera of dinosaurs have been discovered at a nearly constant rate for more than a century, and there's no indication that the rate of discovery will fall off in the near future.
It is more likely that Noah would have brought adults aboard and not babies. The Bible (Gen. 7:2) speaks of "the male and his mate," indicating that the animals were at sexual maturity. Many animals require the care of adults to teach them behaviors they need for survival. If brought aboard as juveniles, these animals wouldn't have survived.
The Bible says either seven or fourteen (it's ambiguous) of each kind of clean animal was aboard. It defines clean animals essentially as ruminants, a suborder which includes about 69 recent genera, 192 recent species [Wilson & Reeder, 1993], and probably a comparable number of extinct genera and species. That is a small percentage of the total number of species, but ruminants are among the largest mammals, so their bulk is significant.
The number and size of clean birds is small enough to disregard entirely, but the Bible at one point (Gen. 7:3) says seven of all kinds of birds were aboard.
Many animals require their food to be fresh. Many snakes, for example, will eat only live foods (or at least warm and moving). Parasitoid wasps only attack living prey. Most spiders locate their prey by the vibrations it produces. Most herbivorous insects require fresh food. Aphids, in fact, are physically incapable of sucking from wilted leaves. How did Noah keep all these food supplies fresh?
Food spoilage is a major concern on long voyages; it was especially thus before the inventions of canning and refrigeration. The large quantities of food aboard would have invited infestations of any of hundreds of stored product pests (especially since all of those pests would have been aboard), and the humidity one would expect aboard the Ark would have provided an ideal environment for molds. How did Noah keep pests from consuming most of the food?
The ark would need to be well ventilated to disperse the heat, humidity, and waste products (including methane, carbon dioxide, and ammonia) from the many thousands of animals which were crowded aboard. Woodmorappe (pp. 37-42) interprets Genesis 6:16 to mean there was an 18-inch opening all around the top, and says that this, with slight breezes, would have been enough to provide adequate ventilation. However, the ark was divided into separate rooms and decks (Gen. 6:14,16). How was fresh air circulated throughout the structure?
The ungulates alone would have produced tons of manure a day. The waste on the lowest deck at least (and possibly the middle deck) could not simply be pushed overboard, since the deck was below the water line; the waste would have to be carried up a deck or two. Vermicomposting could reduce the rate of waste accumulation, but it requires maintenance of its own. How did such a small crew dispose of so much waste?
The animals aboard the ark would have been in very poor shape unless they got regular exercise. (Imagine if you had to stay in an area the size of a closet for a year.) How were several thousand diverse kinds of animals exercised regularly?
Where did the Flood water come from, and where did it go?
How do you explain the relative ages of mountains? For example, why weren't the Sierra Nevadas eroded as much as the Appalachians during the Flood?
How are the polar ice caps even possible? Such a mass of water as the Flood would have provided sufficient buoyancy to float the polar caps off their beds and break them up. They wouldn't regrow quickly. In fact, the Greenland ice cap would not regrow under modern (last 10 ky) climatic conditions.
Why did the Flood not leave traces on the sea floors? A year long flood should be recognizable in sea bottom cores by (1) an uncharacteristic amount of terrestrial detritus, (2) different grain size distributions in the sediment, (3) a shift in oxygen isotope ratios (rain has a different isotopic composition from seawater), (4) a massive extinction, and (n) other characters. Why do none of these show up?
Why is there no evidence of a flood in tree ring dating? Tree ring records go back more than 10,000 years, with no evidence of a catastrophe during that time.
Deep in the geologic column there are formations which could have originated only on the surface, such as:
Rain drops, River channels, Wind-blown dunes, Beaches, Glacial deposits, Burrows, In-Place trees, Soil, Desiccation cracks, Footprints, Meteorites and meteor craters, coral reefs, cave systems. How could these have appeared in the midst of a catastrophic flood?
Much limestone is made of the skeletons of zillions of microscopic sea animals. Some deposits are thousands of meters thick. Were all those animals alive when the Flood started? If not, how do you explain the well-ordered sequence of fossils in the deposits? Roughly 1.5 x 1015 grams of calcium carbonate are deposited on the ocean floor each year. A deposition rate ten times as high for 5000 years before the Flood would still only account for less than 0.02% of limestone deposits.
How do you explain the relative commonness of aquatic fossils? A flood would have washed over everything equally, so terrestrial organisms should be roughly as abundant as aquatic ones (or more abundant, since Creationists hypothesize greater land area before the Flood) in the fossil record. Yet shallow marine environments account for by far the most fossils.
How did all the modern plant species survive? Many plants (seeds and all) would be killed by being submerged for a few months. This is especially true if they were soaked in salt water. Some mangroves, coconuts, and other coastal species have seed which could be expected to survive the Flood itself, but what of the rest? Most seeds would have been buried under many feet (even miles) of sediment. This is deep enough to prevent spouting. Most plants require established soils to grow--soils which would have been stripped by the Flood. Some plants germinate only after being exposed to fire or after being ingested by animals; these conditions would be rare (to put it mildly) after the Flood. Noah could not have gathered seeds for all plants because not all plants produce seeds, and a variety of plant seeds can't survive a year before germinating. Also, how did he distribute them all over the world?
How did all the fish survive? Some require cool clear water, some need brackish water, some need ocean water, some need water even saltier. A flood would have destroyed at least some of these habitats.
How did sensitive marine life such as coral survive? Since most coral are found in shallow water, the turbidity created by the runoff from the land would effectively cut them off from the sun. The silt covering the reef after the rains were over would kill all the coral. By the way, the rates at which coral deposits calcium are well known, and some highly mature reefs (such a the great barrier) have been around for millions of years to be deposited to their observed thickness.
How did diseases survive? Many diseases can't survive in hosts other than humans. Many others can only survive in humans and in short-lived arthropod vectors. The list includes typhus, measles, smallpox, polio, gonorrhea, syphilis. For these diseases to have survived the Flood, they must all have infected one or more of the eight people aboard the Ark.
Why is there no mention of the Flood in the records of Egyptian or Mesopotamian civilizations which existed at the time? Biblical dates (I Kings 6:1, Gal 3:17, various generation lengths given in Genesis) place the Flood 1300 years before Solomon began the first temple. We can construct reliable chronologies for near Eastern history, particularly for Egypt, from many kinds of records from the literate cultures in the near East. These records are independent of, but supported by, dating methods such as dendrochronology and carbon-14. The building of the first temple can be dated to 950 B.C. +/- some small delta, placing the Flood around 2250 B.C. Unfortunately, the Egyptians (among others) have written records dating well back before 2250 B.C. (the Great Pyramid, for example dates to the 26th century B.C., 300 years before the Biblical date for the Flood). No sign in Egyptian inscriptions of this global flood around 2250 B.C.
How did the human population rebound so fast? Genealogies in Genesis put the Tower of Babel about 110 to 150 years after the Flood [Gen 10:25, 11:10-19]. How did the world population regrow so fast to make its construction (and the city around it) possible? Similarly, there would have been very few people around to build Stonehenge and the Pyramids, rebuild the Sumerian and Indus Valley civilizations, populate the Americas, etc.
Why do other flood myths vary so greatly from the Genesis account? Flood myths are fairly common worldwide, and if they came from a common source, we should expect similarities in most of them. Instead, the myths show great diversity. For example, people survive on high land or trees in the myths about as often as on boats or rafts, and no other flood myth includes a covenant not to destroy all life again.
Are flood models consistent with the Bible? Creationists who write about the Flood often contradict the very story they're trying to support. For example, Whitcomb & Morris suggest that large numbers of kinds of land animals became extinct because of the Flood, while Genesis repeatedly says that Noah was ordered to take a representative sample of all kinds of land animals on the Ark to save them from extinction, and that Noah did as ordered. Woodmorappe wants to leave invertebrates (i.e., just about "every creeping thing on the ground") off the ark. Why should we give credence to a story whose most ardent supporters abandon when it's inconvenient?
Does the Flood story indicate an omnipotent God? If God is omnipotent, why not kill what He wanted killed directly? Why resort to a roundabout method that requires innumerable additional miracles? The whole idea was to rid the wicked people from the world. Did it work?