I am also getting this issue. Alfred stops responding to its hotkey after I click on a password field (I have 1password). Clicking the Alfred app seems to fix the issue until I click on a password field again.
Turning off compatibility mode fixes the issue. However, my key bindings depend on compatibility mode (otherwise karabiner can't tell that Alfred is on the foreground). Compatibility mode is one of the top features that made me buy Alfred.
Would it be possible to fix this without having to turn off compatibility mode?
Note to devs: I am available to help debugging this, but looking at the thread I think that the repro steps have now been correctly identified.
This fix would work if I only wanted to trigger Alfred's main prompt but it can't be used to launch other hotkey-triggered workflows. (great idea by the way haha!)