I had a cruiser and two frigates that were only slightly losing. I thought I’d retreat and return with a larger fleet in the next turn.
My ships retreated after two minutes but disappeared off the campaign map! 
I’ll now have to rule the universe with my strike fighters!
I also noticed if the battle is a draw (no clear winner) then I “lose” and my fleet also disappears.
if ships cant retreat within 2 minutes,theyre lost
personally i didnt have a problem with retreat yet… atleast i didnt notice any ships missing
The ‘problem’ with disappearing ships seems to be this: If there is more than one way ‘off’ a planet, the fleet can retreat in any direction, even to a hostile territory. Each fleet seems to make this decision seperately, so with four fleets, you could have 1, 2, 3, or 4 of them make it back safely, or not. If a fleet retreats to a hostile planet, it just disappears. Stupid captains.
my fleets always automatically retreated to either the planet they came from or to a adjacent friendly planet, must be your local problem
It’s mostly working now. Most curious.
Do you have version 1.48 or later?
Says full 1.49 but Ignore my 2nd post in this thread - I was in the red when the battle timed out so technically I lost and my fleet should have been wiped out.
See my other thread - I’ve created a nice bug list for you. 
Enjoying the campaign.