@tkadlec had a great blog post on debugging layout shifts with WebPageTest that also included a sample code snippet that you can inject into pages (Advanced tab of the advanced settings has a script injection box). You probably also need to set a “minimum test time” (be generous like 60 seconds).
With the script, it will scroll the page every couple of seconds after the onload so any shifts that are a result of scrolling will show up in the WebPageTest result.
Lazy-loaded images, injected ads, that kind of thing is a common cause of layouts shifting from scroll.
If the shifts are from other types of user interaction (clicking on a menu) then it won’t pick those up.