When an object is deleted from the scene, is it still present somewhere in the Blender file? For example, I've been playing with physics constraints, so I created and deleted a bunch of cubes. So now even though there are only 2 cubes and one constraint in the 3D Viewport and the Outliner, there are dozens in the object drop-down (only a few fit in the window).
That wouldn't be a problem by itself, but I noticed that the Rigid Bodies behave strangely after creating and deleting objects and constraints. It seems that those "phantom" objects are interfering with the physics engine.
Is this the expected behavior?