Let me start with a problem which recently happened to me when posting my last interview: I cut and pasted an interview excerpt from an email into a post and without realizing it, the transfer caused some of the words to become fused together. Needless to say, the author caught it when they went to see their new interview and I'm glad they did...RULE #1: "Extra eyes can catch many things!"
I've recently been given a PDF where the editor was a professional editor and yet somehow the errors from the old PDF have come into the new PDF. The publisher was shocked to find this was the case, but evidently this can happen...my advice is RULE#2: "Proof the final edit with a new pair of eyes. Even the pros can make mistakes!" And may I also add RULE #3: "Reading your final edit ALOUD can catch things your eyes will pass over. Remember, you read with your eyes much faster than you can read with your mouth. So, you are forced to slow down and verbalize what you are seeing. You'd be surprised how many things will appear when you use this technique. "But, Podlingmaster, I have to rush my book to print so I can get my share of POD reviews and grab my .000005% of the book market!" I know, I know...but patience, little grasshopper.
Exaggerated margins or too much space between paragraphs. Now this one, it would seem to me, would be a simple matter for the author to gauge at the onset. Just looking at books in bookstores you will see the way that books are generally formatted. Yet, on a number of occassions, I've received novels that had double spaces between nearly every sentence. This creates alot of blank space on a page and looks completely unprofessional. Remember, when you format for the pdf and printing that you need to put everything into single space with generally four spaces between P.O.V. changes. And watch those margins folks. Don't try to exaggerate them to give your short story more pages to make the book appear thicker.
Indentations which either have way too many spaces or not enough. Generally, you want about five letter spaces for a paragraph indentation. Now, I'm not being dogmatic...go check the grammar manual collecting dust in your closet for the hard points, but what I see many times is up to ten spaces in a paragraph indent or as little as one space...which by the way almost looks like you can't tell where a new paragraph begins.
Watch out for the common (it's/its--there/their--then/than) stuff as well. And of course there are the missing words or extra words that crop up in a manuscript. Once again RULE #1 prevails here: "Extra eyes can catch many things!"