Not sure if this is a glitch, but the simulation freezes whenever you click a popup that prompts the user to pay with Darwinium (ex: a comet, the yellow orb thing, nanobots in the 15 minute wait time, etc.). All generators stop and don't collect items until the user closes the popup (meaning completely frozen: closing the popup doesn't give the missing loot). Some darwinium payments don't do this (like a boost), but most do.
I've tested this in 3/4 of the current simulations, and they all have this issue.
I'm using steam, if that's any concern.
#Simulation freezes when clicking popups
drowsy steeple
spiral basin
what's your game version? can you try updating your game to the latest version and see if this problem still occurs.