When the bug is triggerd, you can already see symptoms of it when opening Alfred's popup, it will always flicker on opening, and sometimes end up in non-visible state even.
In attached screenshot, I try to open Alfred a couple of times, first few times it just flickers and doesn't show up. Next time it shows up but the focus bug would still trigger on trying to paste content of saved clipboard.
(Gif is not best way of showing the problem but I had to fit within file upload size limit)