I noticed initially that I was unable to open certain Applications from Alfred. I refreshed the Application cache and rebuilt OS X Metadata from Alfred preferences to see if that would solve the problem but then was unable to locate any Applications at all. I was forced to include the Application folder within the search scope in order to find applications at all which I didn't have to do in the past. Unfortunately, this is far from ideal because this also throws in non-Application files from Application folders (ie: Adobe app folders) and convolutes my searches.
Note: I am running Alfred 3 and I did upgrade to El Capitan a month back. No plans to upgrade to Sierra until I can make sure all my work & productivity apps work fine.