I just came into the same problem following heartbeast's platformer game tutorial. He adds an area 2D and it comes into the scene as a 32 X 32 box. Perhaps it was an older version of Godot; anyways, following the tutorial, you then add the godot icon, move the Area2D elsewhere on the screen, then add a collision shape2D and adjust the Extends to 32 X 32. This seems not to work. The problem is, if you try to follow these steps in a current version of Godot, you have moved icon.png from it's parent location, so you're not actually looking at the Area2D which is still up in the left corner of the scene.
Not sure if that's the same issue, but hopefully this helps someone.