Since the patch I’ve had this happen to me twice, had never seen it before. The first time, I was playing Slim in a random Hunt match and I earned progress towards Hyde’s 3 star Toxic Grenade mastery. The second time was during a Defend match in evacuation - while playing Torvald, I earned progress towards Slim’s level 2 Leech Gun mastery. I hadn’t done any Hunter swapping or such in game.
Yes, while running Sunny and Torvald I kept earning progress towards Slim’s gun as well.