Related pitfall: you work for three days on a manuscript that has serious issues, pouring your heart and soul into wording everything as technically and kindly as possible, and the author gloms onto the 'but what about my pov? Should I change it to first?' or some other single, relatively issue that's often a non-issue. One author swore she got 'ten pages of formatting instructions and nothing on content.' Um, I kept a copy of the critique. There was one paragraph of formatting issues with a link reference for guidelines, and about eight pages of content review. Maybe it's a defense mechanism. I dunno. But over the years I've learned to avoid this pitfall by critiquing according to writing experience. If there's a lot of experience, I let 'em have it all (but still nicely.) If it's a newbie, I'll focus on no more than three issues and spend no more than a half hour on the critique (excluding reading time) and end with "if you'd like more comments just let me know." It's not worth the aggravation and I'm not convinced that the newbie can understand more unless they're really astute, in which case they'll ask me for more info and I'll gladly then spend the three days or three months or whatever it takes to help them.
I want to add that there's nothing in the slightest bit wrong with a newbie that can't understand more (or is simply overwhelmed). We've all been there. It can be destructive if you try to fix a gizillion things at once regardless of your writing experience unless you decide to rewrite it from scratch.
Another few of pitfalls:
The writer trusts you more than themselves and makes a mess of the manuscript based on what they think will please you.
The writer decides the manuscript is worthless because you didn't love it and dumps it in the trash, never to work on it again.
You make them cry. BTW, sometimes someone just has to let it all out. Try not to feel bad, and try not to make them feel self-conscious. Assure them that this is a normal response and then take a few minutes break. Bring them water and kleenex, and then start again. This is one of those getting back on the horse things again so really encourage them to listen to the rest of the critique even if it's hard. It'll be worth it in the long run. Exception--the reason they're crying is because they're being subjected to a cruel and personal attack, at which point the critiquer needs to be uninvited to the critique session and asked not to return until they've found their inner professional human being.
Don't be either the critiquer or the writer in this bad situation--you critique and then you expect that the writer will change everything according to what you say. Worse, you become attached to the manuscript and want to see 'your work put to use' as soon as the writer is done rewriting it so that you can help with the final polish. After the critique, hands off! It's even worse if the writer enjoys this interplay. You create a reward/dependency that's destructive for both of you. This is different than feeling satisfaction that your comments were helpful and curiosity about what was employed and where. It's the difference between having your mom help spiff up your apartment vs. your mom 'helping' redecorate your apartment with stuff she got for you.
There's others but I can't think of them right now. Maybe I'll come up with more later.