When a mod deletes a reference that does not belong to it, the game has a tendency to crash on exit (because it is trying to unload objects that no longer exist). But that is not the worst of it. If your mod deletes a reference, and then ANOTHER mod comes along and edits that reference, this will cause the game to crash when it tries to load that reference. So, say mod A deletes a rock in Whiterun to make room for a new building, but then mod B comes along and moves that rock somewhere else for its own purposes. If you use mod A and mod B together, your game will crash when you enter Whiterun because mod B is trying to edit an object mod A deleted.
Finally, in Skyrim, if you delete an object in the Creation Kit, there is a chance that it won't actually be removed, but instead moved to the 0,0 position of whatever cell or worldspace they occupy. This bug is new, while the previous two potential crashes have been with us since Morrowind.
So remember, NEVER delete objects that don't belong to your mod if you can help it. Instead, flag the reference you want gone as "Initially Disabled" and, if you want to be very sure, set its Z position data to -30000. But NEVER delete it, or you open the floodgates for all sorts of problems. ONLY delete references that you are certain belong to your mod.