I've been working on writing a report with a colleague the last few days (I'm sure everyone was missing me terribly) and we've both been a little thrown by the nitpicking we're doing in the final proofreading. It's a little fascinating how we can come back with 2-3 errors per page each, but no overlap, and we've managed to do just that several times now.
For instance, she is a complete punctuation stickler whereas I am an inveterate comma abuser, and I'm very fond of semi-colons, Vonnegut notwithstanding. She'll send me back a passage highlighted and corrected, and I'm asking "huh, what was wrong with that?" and even with her standing over me pointing at the screen with a pen going "look, here!" I still can't see the problem. Or, my version and her version look equally fine to me, so I just go with hers since she is the one that's sure about it.
On the other hand, word order and word choice really bother me when they are wrong. Since we're both writing in a foreign language, this is probably more forgivable on her part than my comma abuse, but let's not go there. There was a post earlier this evening about someone putting something in a "vanilla envelope", but I'm pretty sure my colleague would read right through that. I looked at a book recently where the characters in a trial setting were character witnesses "collaborating" good uhh, character (that sentence got away on me a bit.) In our report, there was one place where my colleague had managed to get the word "advancing" into a short, maybe 5 sentence paragraph, more times than there were sentences. Nothing a quick rearrange and rephrasing couldn't fix, but I found it utterly jarring and she thought it was at worst "slightly awkward". Then I think about books like "Real", or any of the other various poorly written/edited books around doing just fine, and it occurs to me, there must be a lot of people who simply read right past poor word choice, and see the word intended, not the one on the page. Or there are in fact very many people who think they really are called vanilla envelopes.
Another thing that bugs me very much, is when an author takes something I know about, or a place I'm familiar with, and messes it up. Having characters walk improbable distances in impossibly short times, is a common one, in a couple of cities I know well. Just because it's a half mile as the crow flies, doesn't mean one can walk it in ten minutes, on say Stockholm's winding and ancient cobbled streets, in the snow, and when it involves crossing two bridges that are most definitely not going in the same direction that crow is flying.
One I've seen mentioned often is anachronistic cursing, particularly in fantasy novels and sci-fi, whereas that doesn't bother me in the slightest, particularly military fantasy/sci-fi. I've spent more than enough time around soldiers to be quite sure that a thousand years ago, and a thousand years from now, they will still be both flinging around euphemisms for copulation and defecation with abandon, and taking multiple deity's names in vain, so why wouldn't they be in fantasy settings. Yet I've seen readers who can't get past it, and will put a book down or review it harshly. I saw a book reviewer take off a whole star once for the author having used O.K. instead of Okay, or perhaps it was the other way around.
The problem for authors I guess, is that we don't all have the same pet peeves, and some of them are fairly unreasonable. That said, a lot of these are in the domain of good editing, and that's as good a reason as any to get some professional editing done - if you are going to alienate readers, have it be for reasons of plot or a conscious stylistic choice, not because you are doing it flat out wrong.
For me I guess it's much as Mr Darcy says, my good opinion, once lost, is lost forever. (n.b.: I'm quite sure Mr Darcy was fond of commas too). It's as if I open a book fully intending and hoping to like it very well, and once I get immersed in the story, I tend to get to the end and close the book having done just that. So anything that throws or pulls me out of that place of immersion and reminds me that I'm just reading a book, somehow makes me lose a little faith. And then I am disappointed in the author, because they "had me at hello" and then went and lost me.