Since the June patch, I have un-subbed all the Workshop Mods and deleted my own mods. I have tested this again with the following results. If the unit is the only thing in the queue it will update and continue producing it. If however you have anything queued up behind the unit, it will dump the unit to the back of the queue and occasionally dump it completely out of the queue. This happens 100% of the time.
The thing I find amusing and a little incredulous, is that this bug has appeared in every civilization game in which a queue existed. They were later corrected by an expansion or patch. As I fully expect this bug to be patched eventually.