Minor Plot hole: At the end of the movie, one of the Ark's rear door created with thousands of tons of solid metal is not able to seal correctly because a traditional hose felt in-between two dodge caravan-sized gears. This however does not stop a child from removing it later on....underwater. Furthermore, the body of Dr. Gordon Silberman also fell in-between those gears and did not stop the mechanism.
Minor Plot hole: The Arks function very differently from cars. Indeed, if a door is not closed, the engine won't start. Which is not totally efficient when your ark is going to crash into Mount Everest. The engineers in charge of this should be fired....although they are probably already dead.
Minor Plot hole: In the movie, the United States Government needs the help of private capital from rich individuals to fund the construction of 5 big boats. This is the reason why most of the survivors on board of the Arks are rich people who paid for the boats to be constructed.
This is however nonsensical because the end of the world is coming. The government does not need to get rich individuals to pay for their own expenditures, they can simply create their own money and drive their debt even further down because their country, and markets, and current account deficits won't exist in 2 years after Earth is completely flooded.
Plot contrivance: Near the end of the movie, Jackson Curtis and the other heroes crash land in the Himalayas at night. Their chance of survival was minimal since the cold weather would have killed them in a matter of minutes. Surprisingly, a Chinese rescue them, who just happened to be nearby, arrived on the scene to save the wealthy Russian family. And then surprisingly, a Chinese worker in his car just happens to be nearby and saves the other heroes.
Unaddressed Issue: When the heroes manage to shut the hatch and fire up the engines on the ark, we see exhaust fumes coming out of the ark. That's right, because the geniuses who designed these things thought it would be a good idea to run them on fossil fuels after the whole world had been blown to hell. Nah, I'm sure they will have no problem finding a gas station.