I've played a few games of Sins in the past week or two (after not playing Sins for a few months), and seemed to have noticed this bug.  A few times I will queue orders to destroy a few structures to a group of ships, and I'll come back to them a minute or two later and they will be doing something completely different and my command queues are now gone. 

I've definitely noticed it when queuing orders to a subset of ships within a fleet.  For example, I had a fleet nuking an enemy planet.  I ordered the non-capital ships to knock out 5 enemy structures on the other side of the planet.  They got the first structure down to about 20% and then ignored my orders and tried to go back to the main fleet. I had not ordered any new orders to the fleet itself, so this seems like a bug (unless this is a "feature" of fleet behavior)

I'm also 90% sure I noticed this with an a fleet as a whole as well.  I've queued a fleet to take out structures in a specific order, and later it seemed they ignored it and went back to attacking whatever structures or ships they thought was best.

Has this happened to others before?  I've noticed this in both v1.16 and v1.17.