"Well," John says, licks his lips, and shifts until his back is against the wall and his arms crossed. "I'm not sure what to think. But that's nothing new, with you. I don't hate you. I mean, if you actually do start picking me apart, we might have a problem."

Trying to joke it off, that's the best way to deal with this sort of uncertainty. He might just take it as hyperbole, for his own sanity more than everything else. He doesn't know how to interpret it, or if he's doing it right, and if he asks Sherlock... He doesn't think that would go over very well.