Early in a game I found a system with 2 independent colonies (hostile pop's) and a pirate base. Quick ordered 3 Destroyers and 3 Transports for a small conquest fleet.
2x DD's and the 3x Transports built immediately, the third DD is stuck with 6 systems unbuilt, additionally the 2 built DD's fuel slowly trickled away, and now they will not respond to a refuel order. I issue a 'Refuel and Repair' and it instantly goes back to 'no mission'.
So I then removed the 3x DD's and added 3x Cruisers which I could then build, conquered the two colonies and pirate base. Now when I issue a refuel order the Transports fuel up and the Cruisers are sitting on empty tanks and having to slow boat around.
The Civilian side ships, escort/patrols, freighters, explorers, construction, etc... all fuel normally. Military ships will not the instant I add them to a fleet.
Finally quit the game, started a new one, and ships fuel normally. Very weird behavior.