It happens to me a fair amount too...seems like its the closer you get to Fred space. It only happens in solo missions for me.
It's an annoyance, certainly. I haven't noticed if it's just certain missions. I know it happens in planet assaults on the Neutral Zone planets...
Another bugged thing I heard about was a Klingon pilot getting fast drones in mission and then being able to replentish them at the supply dock. Once he downgraded to medium speeds, he wasn't able to buy them again. So...it looks like one of the scripts has a propensity to give human players out-of-era drones which can continue to be replentished at supply dock. Best fix here is to call the mission bugged if it happens in PvP situations and then the players just needs to downgrade back to drones that are correct for the current era. Just a heads up...