I definitely did.
Maybe the bug has to do with destroying the two flagships in two separate engagements in the same battle? I destroyed one flagship, then retreated to reload torpedoes, then destroyed the other flagship.
Here's the what I remeber drom when this happened:
There were two bounties at Mors in Corvus, one by Tri-tachyon, another by Independent.
I have Tri-tachyon commission and is cooperative with independent, and hostile to everyone else.
When I approached Mors, a Hegemony patrol that was keeping contact with my fleet got sandwiched between me and the bounty fleets, and got attacked by both bounty fleets. I don't think bounty enemies were destroyed because the the patrol has only two Enforcers and a Gemini which lost rather quickly, while both bounty fleets had two cruisers.
After the patrol got blown up, I get i to battle with one bounty enemy, with the other one being able to reinforce it. Both bounties have cruiser flagships, one is a Dominator D, the other is a Eagle D. I did bot check beforehand whether the officer names match up with bounty names though.
In the battle:
1st Engagement I used one Afflictor to blow up a bunch of friagtes and carriers, then retreated to reload
2nd Engagement I used one Afflictor and blew up the Eagle flagship
3rd Engagement I deployed a big fleet and blew up the Dominator flagship
4th Engagement is a pursuit, some fighters escaped.
Maybe destroying he two flagships separately has something to do with it?