I'm afraid that's probably just a Rampant issue. Bob's Enemies does not alter enemy AI behavior from vanilla, so anything Rampant does to override that should work the same with BE and without. Also, the nest replacement scheme that I (part of the Bob's maintenance team) created for it is designed to turn off automatically if Rampant's new enemies are in play.
I've also noticed Rampant struggling in the late game, though. Particularly when Rampant enemies have damaging stickers (persistent effects) such as those inflicted by Plasma Cannons on them.
I suggest that when you notice lag occurring, you use F4 to open the debug menu, choose "show time usage", and see if anything stands out as a source of lag (stickers should be listed). Then report to the Rampant/Rampant Fixed team about it.