@abraver Looking at your sample process, you have a workflow using a Run NSAppleScript object.
This object's config sheet specifically warns that it runs scripts on Alfred's main thread, which can block Alfred. The intention of this object is for super quick snappy one shot AppleScript calls, not scripts which could potentially block.
Search through your workflows, and replace the use of this object where appropriate with a Run Script object set to osascript instead, and your issue will be sorted
Cheers,
Andrew