1) Put any extension in your overflow menu
2) Disable that extension from the Extensions Panel
3) It will disappear from the Overflow Menu, as expected
4) Re-enable that extension from the Extensions Panel
5) The extension's button will reappear in the Overflow Menu but also on the main toolbar
In this situation I think the extension should only reappear where it was last placed (the Overflow Menu) and not on the main toolbar as well. But regardless of where it reappears, it definitely shouldn't be happening twice.
Version 0.99.126.4.1.5-rc (WebKit 619.1.1)
Sonoma (14)