#2: Punctuation errors.
I don't mean the occasional typo. I mean three missing commas in one sentence.
When I was a kid, if I handed my mother work I hadn't proofread myself, and she found an error, I was in for a scolding and then sent back upstairs to re-do it. "Read it out loud!" she'd holler after me. It was not fun. I grumbled. I put my head on my desk. What a tyrant! But to her, to give her something with obvious errors which I could have caught myself was lazy and rude. I was wasting her time instead of doing the best job I could.
Thankfully, the lesson eventually sank in.
When I see a query riddled with punctuation errors, I consider two options: either the poster didn't bother to check their own work, or the poster actually does not know how to punctuate. Either way, this is a bad sign for a manuscript, because no matter how brilliant the story, there's absolutely no way I am going to wade through hundreds of pages of comma errors. I've done it, and it's soul-suckingly awful unless you're getting paid for it. Which your agent isn't.
If you're having trouble with punctuation, I strongly recommend the time-honored tradition my mother taught me of reading your work out loud. If this doesn't work, buy/borrow a grammar workbook and work through it, and then read your work out loud. If that doesn't work, hire an editor. :)
Remember, we all lose the occasional comma. But when it comes to queries, you've really got to put your best foot forward!