I figured out what is going on with the levers in the tentacle room. The lever on the left side of the room has a sprite of a stand without a lever that gets a yellow lever once the red lever on the right is activated. HOWEVER, the yellow lever no longer responds after the red lever is flipped, meaning you become soft-locked if you don't activate the left-hand lever (stand) first, which is counterintuitive due to the fact that the sprite is a lever stand missing a lever.
The Switch in the RPGMaker code for activating the left-hand lever is called BreederCaveSwitch1. If you know what I mean by that, it is possible to activate the switch by changing that value to true.