From what I've read it's a glitch in the install procedure that fails to remove the old entry in add/remove.
Assuming that the newer FF got installed to the same directory as your old one, I don't think you have to worry about extra files taking up disk space, since both versions use the same files. If this wasn't the case the 2.0.0.3 uninstaller wouldn't remove the newer install.
Personally this have never happened to me so I don't think you need to be overly worried about FF entries accumulating in Add/Remove.
Btw. personally I've always hated the way Java updates. Each install takes up 70+ MB, so if you got auto update on and don't uninstall the previous versions they can easily take up a lot of disk space.