I had begun to think that my keyboard was broken recently. I popup Alfred and type something along the lines of 1000/10 to do the math and instead I was just getting 100010. After a while I noticed that a notification was popping up saying a macro failed. The macro was failing for the app under Alfred (and the current active title bar). If I wanted to type the slash (which was assigned to a macro in the current app) into Alfred I had to click away from the app first.
I would really appreciate if Keyboard Maestro could detect I was typing into Alfred and direct the keys into that app rather than intercepting them in this instance.