why are they there

ok so i was in the ice town and i look down and see kabutops under ground why is that

 

Kabutops cannot be found in the wild, it was probably someone else pokemon just glitching through the floor.

 

Actually, I think you are talking about the Team Mystic base. There is a secret base for team mystic somewhere underground where water pokemon NPC's are. You can still see their nametags above ground though..