Originally Posted by Fat Death Phenomeno
Can anyone confirm if this still happens in the sequels?
It does indeed still happen; both a Skarmory and a Jumpluff holding Iron Ball took neutral damage from Mud Shot when used on them.
On a somewhat related note, I haven't seen it mentioned in this thread but the Sky Drop glitch still exists in B2W2, as well as Sheer Force boosted moves negating Life Orb recoil, among other things. I'd wager that Game Freak didn't fix/change any battle mechanics just to preserve Wi-Fi compatibility between the prequels and sequels. I wouldn't mind if I'm wrong about this though.