The error stopped after redoing the collision polygon.

As for the holes (pools of water), I set it up so they have their own collision polygons, so I can then check collision with areas in the "water" group. The land has its own "land" group, which will allow me to check if the player tries to exit it. If the player is on land and not in water without a boat, the player is fine.
Hopefully things will work now!