I installed Alfred 1.2 from the App Store. Then realized that the newest versions were not being installed via the App Store, so I deleted the App Store version and installed Alfred v2 from the web site.
Current setup:
* Alfred 2.8.3 (435)
* OS X 10.11.3
So the bug is: I have Parallels Desktop installed (normal install; app is located at /Applications/Parallels Desktop.app). When searching with Alfred it will not find Parallels Desktop. Typing "par" locates only "Parental Controls". Typing "parallel" just prompts me to search the web. Ditto "parallels desktop".
I checked Spotlight. Spotlight finds the app if I type "par" or "parallel" just fine. To be on the safe side I rebuilt the Spotlight metadata index yesterday, which resulted in no change to Spotlight's ability to locate Parallels, nor in Alfred's inability to locate the app.
I also checked several other apps that are installed. Alfred found all of them without incident.
I use Parallels quite a bit and it's awfully frustrating to have to switch to spotlight or Launchpad to open it when I'm used to opening everything via Alfred.