Defiantly a minor bug.
I just tried on 1.46 W7x64
steps:
1) added PI sort CSS
2) restarted Calibre
3) opened editor: On the Menu: Plugins: Sort CSS appears, no other toolbar
4) (in the editor) edit: Preferences: toolbars: Book wide from 3rd party.
appears
<the trigger event>
5) (in the editor) edit: Preferences: toolbars: Book wide : Add sort CSS to this toolbar: OK

2 copies of the Icon appear
6) remove the icon in step 5: OK

One icon is left