Separating ships with damaged engines seems to not always be working:
In the provided save, in the "WX Ursae Majoris" system, I am fighting the Star Swarm. Earlier I let off a salvo of box launched missiles at a FAC swarm. There were at least 20 FAC that have working engines, but are in a fleet with FAC that have crippled engines, so they aren't going anywhere. As a result, I am able to just fly up and kill the still functional FACs, even though they should be able to chase me down.
It took me a while to realize, so I have been picking away at them for a while now with some cruisers, but I am confident that some of the FAC in the big group of 50 still have working engines, and thus shouldn't just be sitting there and letting me kill them
SJW: I have seen this too, but not tracked it down yet
Edit: Bug Report 2: I just realized that I have colliers in "Battle Fleet", but they aren't reloading my carriers, despite being set to "Load Fleet Ordnance". So that is also in the same system and save.
SJW: Do you have Underway Replenishment tech?