Here's a couple more reasons:
Lack of genre focus. Agents get queries all the time saying that a book might be this genre or that genre because the writer has utterly no clue what it is. Um, if you wrote the book, shouldn't you know what it is?
Too long/too short. One agent says that if he sees a book that's 150K, his first thought is that the writer isn't finished writing it because they didn't edit it.
Rehash of existing ideas. One editor said he would like to find another "Harry Potter" and had to quickly add that he wanted a book with the same kind of magic for readers--not books about brooksticks and magic schools.
Nothing happening. It's very common to see a book where the writer spends fifty pages just trying to settle into the story--all the while, no story is happening.
Don't know what the story is about: You'd be surprised how many don't really know. This one is actually pretty obvious in the query letter. The writers will start talking about events and backstory but never get into what the story is about.
Pitching the wrong kind of story: If the agent takes sci-fi, don't send him a romance. If he only takes non-fition, don't send him fiction. Yet, people do it all the time.
Not paying attention to the rules: This was from an article on POD. The writer packaged her entire manuscript up, sent it to a publisher, and got it back unopened three days later (at which point she gave up and went POD). If she'd done her research, she would have known that she shouldn't have sent the entire manuscript to a publisher.
Gimmicky: Sending a shoe for "foot in the door," black paper with red ink for horror, etc.