SPOILERS:
1. Thousand foot high waves don't move across 2ft deep water without breaking. Also, lame camera tricks prevent the astronauts from simply scanning 360d and realizing there's a huge wave bearing down on them. Also, there was no reason whatsoever for Doyle to die on the water planet.
2. Too emo. Too much bawling and crying, too much emotional decision making, the actors weren't convincing as trained scientists or disciplined test pilots. The audience actually burst out laughing when Mann and Cooper got into the fight on the ice planet, and when Cooper just let Mann bash his helmet in a couple times instead of pulling away like normal person would. See 2001: A Space Odyssey and The Right Stuff for how such people should be portrayed. Artistic integrity sacrificed for artful, faux emotional appeal, SOP for Hollywood these days.
3. When Mann crashed the shuttle into the mothership, then Cooper and Brand saved the mothership, one second it was over a planet, and not the first planet they visited that was really close to the black hole but the next one out. The next instant they were in danger of falling into the black hole. Months or years worth of distance traversed in seconds.
4. Cooper saved Brand by dropping both TARS and himself into the black hole, giving Brand on the mothership enough velocity/lack of mass/whatever to escape the black hole. The time dilation effects of him dropping into the black hole should have meant he and Brand diverged greatly in age, yet the end of the movie showed him taking off to go find her, same age.
5. The premise of the movie is that future, advanced, five-dimensional humanity was using its power over gravity, time, and higher dimensions to help humanity of the past survive the dying and 'Marsification' of the earth. But the paradox was never resolved - if humanity of the past couldn't survive on its own, how did it ever become humanity of the future? I suppose they did that on purpose to let the audience have fun debating it afterwards.
There were a few others I can't remember atm, but you get the gist. Some of these, like #3, I suppose have to be done to cram the whole story into a 2hr45m movie (another cool thing about it - nice and long), but others were just annoyingly pointless.
But again, overall it was good, worth watching, and having Kip Thorne co-produce helped a lot. Just don't expect perfection, even with his name in the credits.