This usually happens when you download/apply an update to a mod. Say you download Mod 1, and an update for it, Mod 1.2, so you have them both in the downloaded section. You install Mod 1 and call it 'My Mod', then install Mod 1.2 but also install it to 'My Mod', overwriting whatever was in Mod 1. Now if you uninstall/remove 'My Mod', then Mod 1.2 will show as uninstalled, but Mod 1 will still show as installed. Best way to avoid it, if its that big of an issue for you, is to install them seperatly and NOT overwrite the existing install, but install it as a new mod and have it below the original in the left hand side window