I'd suggest that for the boss levels, make the babies spawn a bit quicker? (At least the blue room - mines area) Because an enemy could slip by pretty easily and you wouldn't have anything on hand to stop it, id say all the (first loop) regular levels were pretty good to control but when it came to the first wave of the bosses, that part nearly killed the run everytime.
(Btw the concept of this game is genius, so just props to you for creating this, it's amazing)