The drinking scene
I really like this movie, but the scene of Short taking a drink and Quaid taking some of it into a flask really annoys me.
Quaid's body wouldn't be able to process anything received from outside the pod while he was shrunk down. Biological processes are dependent on molecules interacting with each other in specific ways. If he were shrunk down the way he was, the molecules in his body would be shrunk down also, and they wouldn't be able to interact with the molecules in the alcohol. The alcohol molecules would be too big to enter into chemical bonds in his body. This is also why he wouldn't be able to breathe if he popped the hatch in Short's lungs. The oxygen molecules would be too big to bind with the blood cells in Quaid's lungs, and he'd asphyxiate.
None of this affects the movie in any way, and I really do enjoy it on the whole, but I can't stand it when people don't think everything through when they write a scifi movie.