I believe you are right Javier, I had similar problems with the isometric pathfinding app, from letting AppGameKit try to find the tile shape automatically with 12 points with SetPhysicsMaxPolygonPoints to setting my own points manually in different ways I tried it all and still ended up not understanding why there were areas of the tile being ignored by GetSpriteHit.
One of the last version's updates referred something like "Fixed polygon hit test bug" but the problem I had remains.
Hopefully this will be fixed in a future version