This happens to me once a day at least. I work almost exclusively in fullscreen or split screen on macOS 10.15 and I use alfred for just about everything. The macOS switcher is broken at times, switching to the wrong window, etc, and so I just use alfred.
When I open my laptop, the computer switches from single screen to double screen mode, and the Alfred bezel will not show up anywhere. I can activate Alfred, and the window focus changes, and I can type text and it'll do what I want, but I never get to see what I'm doing. Switching between windows the bezel is almost never active long enough that I care, but navigating any workflows, clipboard history, or anything else is impossible.
The only preference I can see as relevant is: "Show Alfred on" which I have set to "mouse screen"
When I close my laptop, the proper functionality is restored.
I'm sorry to say that the bug presents itself often, but not every time.