This warning only shows when your polygons are overlapping at some point..
Look at the polygons for all objects with the physics behaviour
Look at every frame of every animation if there are more than one frame or animation
make sure there are no overlapping or almost overlapping points within the polygons
change the physics from collision-polygon to bounding box or circle for square and circular objects..
If there are still issues, turn of the physics behaviour for one of the objects at a time to find out which of them is causing the problem..