This is a very interesting thread topic and I find different people's responses quite intriguing. Here's my perception of this situation.
I've been around long enough to know that 'perfection' is rarely, if ever, seen in a custom made cue stick...especially the more hand-made it is. For that reason, I don't generally don't expect it. You will commonly encounter things that are slightly off, glue lines around inlays, very fine finish scratches that haven't been buffed out totally, low spot in the finish where it's slightly sunk into a piece of end grain, etc. If you want, you can pick apart just about any cue as having its issues here and there.
However, that being said and having not seen pictures of this cue that is at issue, this buyer obviously had an issue with the wrap groove being cut too deep (or finish was applied too thick or a combination of both) and ring sets not being aligned. This is most definitely a valid complaint on a new $2000+ cue built by a well-known, seasoned cuemaker. These are most likely errors in the construction and not slight imperfections with the work. But again, we've not even seen the cue so this is supposition and if he is OK with it, that's cool.
Lisa, yes, even Skip is human. However, unlike some cuemakers out there Skip has an excellent reputation for making things right in the event there is an issue. BTW, we finally sold the inlaid rosewood cue you liked so much.
Sean