What code are you using to modify the clipboard?
If you use a timer - make sure that the page is still visible (i.e. that the popup is not closed).
If you use the clipboard API (i.e. adding a listener to the “copy” event and then trigger the event via
document.execCommand("copy")), don’t use just clear the data, but also set some data, e.g.
event.clipboardData.setData("text/plain", " ");.
And note that you are able to copy data to the clipboard from the background page when out-of-process WebExtensions are enabled. Eventually this is going to be enabled by default, but until then, visit
about:config and set