So yeah, I accidentally connected wrong pipes together and didn't notice it. I noticed that water started to pour out of the pipe roughly between those two pumps, when I started to look at it closer to understand whats the problem, game crashed.
Or it might have been the srubber, which is connected to the same system. I'll try to experiment more.
Upd: It was the scrubber, although it worked for ~half a cycle before crash. Dunno what causes it, really.
Connect two pumps together? Or something that outputs liquid I guess.