My guess is it has to do with the sword you get at the end. Or maybe you have to pull all of the three last bosses together…?
EDIT: I got it! I think the first secret is the door in the third boss’ dungeon you can teleport from to the central part the map, the second is the guy in the water, and the third secret is the bunny at way the bottom of the map. After you beat the first three mini-bosses and he leaves that letter, that’s where you can find him.
EDIT 2: I think the three secrets are the blue bird, the man in the dungeon, and the rabbit. Those are the three characters you see at the end when you get all three.