You're totally right about this. In general the efficacy of engines is different for different parts of the game. In the beginning players (and engines) are mostly playing from books so there's a lot fewer mistakes and what the engine thinks of as a mistake is just someone going outside its pre defined book. Mid game the analysis is very effective. In end game the engine can actually completely solve the game, so it really just judges moves as winning or losing.

Spoiler: We're planning to address a lot of this in an upcoming followup I'm working on right now. We're going to take this in to account in our analysis as well as giving people the raw dataset with info about when the blunders occurred so that can learn from it themselves.