I created a 2v2 and the game became a 2v1, with my ally and I still surviving. The Pirates were active and I clicked on the button to increase the bounty on my enemy, but it increased it on the destroyed faction not the remaning faction.

 I had to go into the diplomacy menu, selct pirates and increase the bounty from there. On that screen as well the eliminated faction was highlighted. But the dull button for the surviving faction worked.

100% reproducable...and let me guess..already in the to-be-fixed list? Good!