Cortex Boss Spawning Bug

Suppose you leave the Cortex boss room and return to your hideout while the boss is transitioning phases (exactly when the robot boss disappears and the robed one is about to appear, so there is no entity in the map), when you return. In that case, the boss does not continue transitioning into the next phase, and you'll waste your map.

Leaving and re-entering the map doesn't help.
Relogging and entering the map doesn't help.