Your entire brain does not fall asleep. A significant part of your brain is still working at reduced capacity and some is even fully awake even in your sleep. Specifically the area near your brain stem, in the “core” of your brain, is always awake. This is responsible for a lot of your instinctual behaviour and a lot of primitive behaviours. Things like breathing, temperature control, moving when you are uncomfortable, etc. And this includes your bowel movement and peeing.
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