I just happened to notice that I had a bunch of fighters boarded during a clash with the Swarm.
I successfully landed those fighters, but they were overtaken by the Swarm afterwards. I thought they simply "disappeared" (they were removed from the sub-fleet) so I built newer model fighters to replace them, but when I detached the sub-fleet with the remaining old model fighters (about 12 out of 40 survived the encounter), the "boarded" fighters also appeared in the same fleet.
Now I'm somehow controlling those fighters (that have been renamed and "assimilated"), and they still have the Swarm marines aboard, but I can't get rid of the marines. This is all quite weird, is it a bug?