Peeing on floor when i have toilets.

I had this problem as well. What seemed to happen was my lavatory's state didn't save properly between save/loads and so when I loaded up the game, all 3 of my lavatories were "in use" despite not being used at all. They went ignored and my whole base was full of dupe messes. I had to destroy and rebuild the lavatories before they worked again, simply disabling didn't cut it.