Like probably a lot of people, I’m rewatching “Arena” again, and at first it looks like a clear continuity break (though I wouldn’t care much; it’s TV, they’re allowed). But! Two saving factors quickly become apparent:
1. When Kirk initially chases the alien ship, he has no idea at first that it’s the Gorn. It heads for an unfamiliar area (so we can retroactively assume that the Gorn have quietly expanded to new areas), and is only identified as Gorn when the Metrons refer to it as such.
2. In the planet, Kirk’s faced with the Gorn captain, which he describes in the log voiceover as “a creature the Metrons called a Gorn”. That would traditionally be taken as his never having heard of the Gorn before — but in context, he says it just after first seeing the classic humanoid rubber-skin Gorn for the first time. Which looks completely different from the Gorn Starfleet has encountered before! Hence, “a creature the Metrons call a Gorn”. It’s not that Gorn are unfamiliar, it’s that the Gorn have apparently changed, and that’s why we didn’t realize it was them at first.
So if SNW happens to follow up with a story in which the Gorn mutate or encompass more than one species or something, all will fit — probably even if they don’t.