In the final room were you fight Clone Cop, you can see that Wilson was teleported there as well. That explains why he's in a broken state after you defeat Cone Cop and get sent back to the Entropy Control room. Because he was next to the explosive barrels.
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Also 2 fun facts: -Theres a trigger that teleports you back to your part if you try to jump there -Its also the room where Clone cop kills the teleporting Spider during the halucinations just above