I think the problem is Flanderization. Claire's experienced negative character growth because she and Marten have been reassigned as background characters. When that happens, their most exaggerated quirks tend to be more pronounced. A good comparison is Tai.
Marten has neither hills nor valleys to exaggerate when this happens to him: He's just a cool, nice guy. With Tai it works because she was already an exaggerated character template: She was born a tattooed-punk-stoner-poly-lesbian-erotica-author-librarian. Fantastic character, inherently suited for the role. She can have those exaggerated moments without sacrificing anything.
But Claire? Claire was an intern promoted to Marten's love interest. When she's playing that active role she's a more nuanced, balanced character with subtleties, because she was born for the romantic-drama plotline. But now that that arc is over, we can't afford for her to have the subtleties in the scenes she's in, where she's used as a comedic character like Tai. So you fall to exaggeration to make that work.
I really want to see her have an active story again, for a while, just to bring her back down to Earth. But that would mean other characters losing the spotlight, and they're more interesting to me.
EDIT: Old Goat cites intellect, trans and being a nerd as the reasons she might rub people the wrong way, and I strongly disagree.
We don't actually see Claire be that intelligent in the comic. We know she is, but it hasn't been the forefront of her character in a long time.
Likewise, I find it very hard to imagine people in this forum specifically being annoyed by nerdism -- One Of Us, One Of Us! -- or her gender.