First though, what the film, and the book, got wrong. Probably the greatest, most dramatic error was with the ability of the wind on Mars to wreak such havoc. In reality, the atmosphere of Mars is less than 0.5% of Earth's atmosphere. There is no way it could generate enough force to toss such large chunks of rock around in a dust storm, much less rip apart a radio antennae, or tip over the ascent vehicle. Even at hurricane velocities, there simply are not enough molecules to provide the force required. With that said, Science fiction needs to take the facts and do a big "what if..." number to create the drama and tension. There would not be much of a story without that.
Problem two is that we have just learned, or at least have reason to suspect that the martian regolith (dirt on Mars) may not be able to support growing plants. This is still up in the air and needs further investigation, and was not known at the time of the book's writing, but it may be a problem for future Mars expeditions.
The only other real issue are the scenes on the spaceship where teh women's hair is laying flat and not floating around, even in parts of the ship where there is no artificial gravity. Oh well, can't think of everything.
Other than those, pretty much everything else about the movie is incredibly accurate. The effects of isolation, the dust devils, the geology and landscape, the use of pathfinder, the difficulties he needed to overcome and the way he accomplished it... all were brilliantly researched and developed. In my humble opinion, The Martian is one of the top two or three best science fiction movies around as far as the use of actual science is concerned, and an incredible movie as well.