We have a 2-3 month old kitten at work right now who HATES being scruffed. I'm talking full-out screeching and clawing and hating the whole thing. Otherwise, he's perfectly handleable. He's feisty and mouths a lot, but he doesn't mind being picked up and cuddled and played with.
I know sometimes the backs of their necks can be sore from vaccines, but it's been a few weeks since his last shot and I don't feel any bumps or anything on his neck. And he's not sensitive in that area otherwise, just when he's scruffed.
Do you think it's a physical issue causing him pain, or just him hating to be picked up that way? I work at an animal shelter without a vet on staff, FYI.