I have observed the following behavior on two MacBook Pro models running macOS 10.15.6 and Alfred 4.1.1.
When Alfred is running, sometimes when I switch between already running applications with a mouse click, the app I'm switching to seems to lose keyboard focus and typing any key only results in a system beep.
For example, if I'm in Microsoft Word and change my focus by clicking in a Chrome window, occasionally typing in Chrome will only cause system beeps with every keypress, but no characters appear. The only way to recover is to click away to another application (say back to Word) and then switch focus again to Chrome. I've observed this keyboard lockout behavior when switching between a variety of apps, including Chrome, Word, Firefox, Slack, etc. Also, when an application has its focus blocked/stolen in this way, the mouse cursor also fails to register mouse-over events in the affected application.
This is not a problem that happens with 100% regularity, but during a normal day I'll encounter it multiple times per hour. It happens on two laptops (one 2015 and the other 2019) regularly.
I am 100% sure Alfred is causing this problem because it happens multiple times per hour when Alfred is running in the background, and I have never observed it on the same computers when I quit Alfred. I also never observed this before upgrading to Catalina several months ago.
If there is any way to get more data from system logs or other sources, I'll be happy to try to provide them.