This is mostly a post so that I’ll find this when inevitably I get myself into this situation again.
I’m guessing I was playing with settings shortly after upgrading to the latest MacOS, and I must have clicked Finder’s “Show all filename extensions”. Later, when using Alfred, I noticed it was returning results like “Safari.app” rather than Safari.
I spent a bunch of time trying to figure out which Alfred setting I had ticked.
After a bit of googling, I found this StackOverflow article that pointed me to that Finder setting.
Also, you should buy Alfred. It’s great.