Have encountered this too every fight until my latest game when some Iridium ships did not go invisible at any stage of attacking their stack of three or so ships - so what I thought was a straight bug has now become intermittent it would seem.

I've also encountered this against the Drengi.

They create large stacks of ships, after the first combat the stack seemingly disappears but it is still there. Seems like a mix of fleets and individual ships in the hex.

Once you get through some rounds of combat and whittle down the stack, usually a ship will reappear.

r.

I've this issue too, I attack and the enemy ship disapear, if I unselect my fleet after the attack the enemy ships appear, but if I attack again the enemy ship disapear again.

Thank you everyone for noticing and reporting this! I will make sure it gets to the developers.