Installing/removing the extension packaged by distributions doesn't update the GNOME Tweak's extensions list
Issue was originally reported in gnome-tweaks#98 (closed) - where @jbicha says that the list of current extensions is obtained from gnome-shell.
I got hit by this today, when I installed the dash-to-dock extension from Fedora repository and went to GNOME Tweaks to enable it. It was not there, until I restarted the session. Later today I removed some other extensions that were installed from Fedora repositories, opened again GNOME Tweaks, but the uninstalled extensions were still presented there.