The cluster of three seeds in the middle of the map are behind a secret passage that requires you to kill every Large Cave Slime in the dungeon before opening.
The only time I had success getting the 3 mokokos in the middle was: 1) clearing all the bats and slimes, 2) then hitting that last lever at the end of the dungeon (before boss fight), and THEN 3) going back to get the 3 mokokos... Not sure if the order matters, but that' what worked for me.