Yes, when there is more than one monster of the same kind you'll put a token in there to differentiate between them
Also, for the original Mansions of Madness, they hold the damage a monster had taken (in 2nd edition, that's tracked in the app).
Because of a new base mold, the small bases in 2nd edition don't hold cardboard like the 1st edition small bases did. So for those, it doesn't do much of anything, really. :(