The bug is as following:
Turn on clipboard merging: https://i.imgur.com/Pjcpi3A.png
Regular copying works (⌘+C), clipboard merging works as well (⌘+C,C) After several minutes, however, every regular copying becomes clipboard merging, effectively disabling the clipboard Turning the feature off, fixes the issue
Details:
OS X 10.11.5 (15F34)
Alfred v3.0.3 [694]