Thanks for sharing your state. I just tried again with troubleshoot mode, it works ...

Then it seems to be in conflict with some addon I'm using.

I found that it is caused by a userscript running below code.

    // version 1
    let body = document.createElement('body')
    body.innerHTML = document.body.innerHTML

    // version 2
    let body = document.body.cloneNode(true)

Either version can trigger the bug of the pop up menu now showing up. The menu is able to show up if doing early return to skip that code.

This is wired, that code should not be mutating existing DOM.

Update: Below version of sandboxed clone doesn't break the youtube popup menu.

    // version 3
    let parser = new DOMParser()
    let doc = parser.parseFromString(document.body.outerHTML, 'text/html')
    let body = doc.body