Alfred does not detect applications that are symlinked into /Applications
The case that I am thinking of is MacVim installed with homebrew. Alfred does not allow you to launch it.
What you were doing when the issue happened
Trying to launch MacVim.
Whether you were able to replicate it a second time by performing the same action
Yes
Include any screenshots that might help us
Will not really help.
Include the Alfred version & build number you are using
v2.0.3 (187)
Include your OS X version
10.8.3