For a while now, I've had Alfred's input window occasionally disappear when I was in the middle of typing something. I finally got around to trying to figure out why. Basically, I can do the following too quickly:
1. Quit an app via cmd-Q
2. Activate Alfred (in my case, via cmd-space)
3. Begin typing something
If the Alfred panel opens before the background app quits, when that app does finish terminating, the Alfred panel will also close. The biggest culprit, for me at least, is when I quit Apple's Mail app + Spamsieve. That combination seems to do enough cleanup prior to closing that I can easily reproduce the behavior I'm talking about.
This "bug" is such a minor thing, except when I'm typing in Alfred and the panel suddenly disappears, continued typing is now sent to Finder. This has occasionally resulted in me renaming files on my desktop, which is super annoying.
Anyway, I love Alfred and look forward to seeing it get even better.
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Alfred v2.8.3 (435)
OS X 10.11.4