I noticed this in the first node of the current “Thick as Thieves” story event (“Heavily Guarded”). The enemy team consists of two Hitman goons and a Thug, and I was using the fully covered loaner Valkyrie.
The Bounty Hunter countdown appeared, and when I tapped on it I was told that it was targeting Hitman. There was no indication about which Hitman was the target though: the only way to tell was to try attacking one of the Hitman goons and see if the damage counted. I chose wrong, so the first tick of the countdown tile was effectively wasted.
I guess this is the same problem as other powers that have a “targetting” component when it comes to missions with identical goons.
//Edited Title -Brigby