Seen this a few times now, can't reliably reproduce. I had a modlist with several mods and plugins and ran 'delete mod all'. After hitting [Enter] at the prompt showing which mods were deleted, ammo still showed that I had one plugin, realistic_water2.esp. Refreshing caused it to properly be removed. This means either deleting mods isn't refreshing correctly or deactivating mods sometimes doesn't remove plugins. Not sure which yet.
Seen this a few times now, can't reliably reproduce. I had a modlist with several mods and plugins and ran 'delete mod all'. After hitting [Enter] at the prompt showing which mods were deleted, ammo still showed that I had one plugin, realistic_water2.esp. Refreshing caused it to properly be removed. This means either deleting mods isn't refreshing correctly or deactivating mods sometimes doesn't remove plugins. Not sure which yet.