It depends. If it directly contradicts what the author is actually trying to say - ie. if the author is trying to make a point about X and then does something which implies something completely different, then yeah, that's a huge problem. Similarly if the movie is trying to authentically or accurately depict a historical event (Apollo 13, which I rewatched today, would have been a way less striking movie had it not been accurate in all but a few minor and explainable details), then it's a big deal. But in something like a Batman movie, **** about this or that not being physically accurate or why did they not show how he got from A to B or whatever - I couldn't give a toss about that. That's not why I watch movies.
The lamest thing I saw in the lead-up to the movie by far was some 'study' some guys did exposing how, in fact, Batman's cape wouldn't have actually worked. If this was done in a Mythbusters-esque tongue-in-cheek sort of way then it's cool and fun, but when it's serious (and I think this was), then it's just flat-out lame.