Admittedly, the writing alone has a whole host of problems, but there is one thing in particular I have to focus on. Every single movie I have seen of his has a glaring flaw in the story. They have interesting premises, but the stories end up having horrible execution.
Unbreakable is a movie where, ostensibly, superheroes exist and are unaware of it, and the one person who believed it massacred thousands of people for years just to try to find one.
Signs is a movie about a man who lost his faith coming to learn that his tragedies were signs to show him how to save the world, literally. The problem is that these aliens are so stupid that they invaded a planet where two thirds of the surface is covered in a substance that melts them, and it also periodically falls down from the sky itself.
The Happening is a movie that puts forth the idea that the world is conscious and rejects humanity by trying to purge it. The problem is that this entire movie was a collection of hypotheses with no facts whatsoever. It was a movie so devoid of sense that the characters spent their time trying to outrun the wind, and somehow succeeding.
I can only call this phenomenon Shyamalan Syndrome. It is the affliction where you get a decent idea, and then every time you have to fill in a blank or answer a question, you literally use the first thing that pops into your head without any thought to how it would fit with everything else.
What compounds this issue is that, somehow, it seems like there is no editing going on. There are no continuity checks. There is no common sense checking. The final result looks like a weak first draft to me.
Make sure this doesn't happen to you. Get people to read your drafts. Make sure that when you fill in gaps, you don't betray your existing canon, and don't lack any form of common sense, either.