As posted elsewhere, here's an image of my "
restore"
screen for Beethro and the Secret Society:
As you can see, the game says that I've explored 85% of the level; but I gather from NiroZ that there are no other rooms besides the seven I've gone to.
I haven't especially noticed this for other holds, but one other level of this hold seems to have this problem (again, unless there's some other non-secret, non-required room that I can't find there). In the Entrance Halls, it displayed as 91% Explored at one point, even though there were clearly no other rooms to explore, and the next time I looked it had switched to 100%.