I tried what you described this morning. I found it happened not for the PDF file button but the Paperpile button with the checkmark. I had PP open in another window, searched for something in Google Scholar, found an article I already had in PP, click on the Paperpile button with the green checkmark, and it wouldn't open in the PP window. I had to close the PP window, then the button worked. That window/tab had been open for days. I could add to Paperpile and search on Paperpile.