Not a bug. It has worked this way since day one - bonus multiplyers only for unique troops.
To be honest, all team bonuses in this game work in accordance to this mechanic, so I doubt it should come as a surprise.
If they rework how they give points, they would need to rework the rewards and make them 4x harder to get each. It would be kind of overpowered using 3x or 4x of just bounty captain and it would make every prior bounty release not worth using.
I find this completely misleading and unacceptable. Because then, why bother putting a bounty captain in the last tier shop ? Once you have a mythic captain, why get another one if you can’t have a bonus ?