Well, the one big plot-hole, that was both in the book and the movie was the dust storm that stranded Whatney on Mars in the first place.
The dust storms can be dangerous, due to visibility, and the dust messing things up, but with 1% of Earth's atmosphere, a 200 mph dust storm is like a breeze you can barely feel. Andy Weir acknowledges this though, and said he needed some way to strand Whatney on Mars, and make the rest of the crew leave him by mistake.
Other than that, my only other complaint was the massive amounts of space and huge windows the Hermes had. The spacesuit finger-squirting leak was also a bit overdone, but I guess they had to add drama somehow for the final rescue/capture.