I am using Alfred 2.8.2 (425) on Mac OS X 10.11.2 (El Capitan). Probably at least since updating to El Capitan, Aflred has not been loading automatically at startup or login.
I have other programs like Alfred that only reside in the menu bar, such as Fantastical, Avira, and Toggl. Of these, Fantastical and Avira load automatically, but Fantastical doesn't.
So while this isn't a bug that is exclusive to Alfred, or may not be a bug at all, what is different about Avira and Toggl that they load fine and Alfred and Fantastical don't?