@chermi11, this is a known bug with most managers (eg MM). You can only try to prevent it by ensuring you delete something exactly the way you installed it (eg if you installed it with MM, delete it with MM). Also, it's a good idea to fix permissions before deleting anything. That said, some people misunderstand how much space is actually being used up because there are a lot more things on their HDD than they realise and calculating actual HDD capacity is not as straightforward as most people realise. If you are certain you should have more free space on your HDD - unfortunately - best you can really do is live with it or reformat your HDD.
"We all agree your theory is crazy, but is it crazy enough?" - Neils Bohr