Bug: Commanders are getting reassigned to new ships instead of dying in the depths of space (or possibly in an alien gulag).
After a botched raid against an NPR's home system, my fleet had to run with their tails between their legs - full speed, shooting at volleys of incoming missiles every 15 or so seconds, with a depressing number managing to make it past the railguns to strike the fleet. Anyway, long story short, two ships exploded, leaving lifepods with commanders. We couldn't turn around to pick them up, so left them as the fleet jumped out system.
Shortly thereafter, some new ships were built and I was surprised to see one of the left-behind commanders assigned to it (CAPT Frodo Baggins - memorable enough that I noticed). It is indeed the same captain - his history shows him getting his ship blown up around him (twice, as it so happens, but I picked up his lifepod the first time.)
This is on v1.13.0, with no database hacking or anything else funny going on.