Ok, playing the mission with the Plato. First time through I did all too well. When the Shivans jumped in to attack the Plato, I ordered my wingmen to defend the Plato. They did so. I personally kept the bomber off her and blew it up, but only shortly after seeing "bonus objective completed". When I looked, the Plato had made it to the jump node.
Second time through, my wingmen for some reason didn't correctly engage the Vasudans, so I was left way out of position when the Shivans jumped back in to attack the Plato I didn't order my wingmen to defend the Plato this time so that it would be blown up. After it was, and all but the one Scorpion jumped out, I and my wingmates blew it away. Completely successful outcome, but no bonus objective complete indicator during the mission.
Was that bonus objective not in the original mission?