My "official" theory (that is, the one I put on
memory alpha) is that Burnham's mutiny didn't count, because it was a failure with no crew support that had no impact on anything.
My unofficial theory, though, is that the scene from "The Tholian Web" is an example of Spock's most savage brand of dry Vulcan sarcasm. Chekov impulsively asks the room whether there's ever been a mutiny on a starship before because he's a young man who talks before he thinks;
of course he knows about the infamous Battle at the Binaries. Everyone else feels super-awkward about the question, because
of course they know Spock's own adopted sister is Starfleet's most famous mutineer.
Chekov realizes this about two-thirds of the way into his question, but by then it's too late for him to stop. To prevent the whole thing from settling into an awkward silence with everyone staring at him, Spock sarcastically deadpans that nothing like this has ever happened before, then gives Chekov a look like Pavel is a small bug and mentioning Burnham will get him squished. This resolves the tension, and everyone is able to move on.
Chekov's embarrassment and shame about the exchange is what predisposes him to become the
Enterprise's first victim of interphase madness.