Yes - if two players deliberately just ran straight into each other when the ball was going in a different direction some way away, the ref would blow and give them both a telling off for fouling each other.
For the umpteenth time, this is not just "a pen being given because a defender has shoulder barged an opponent in the box", it is wildly different to what any normal person sees as a shoulder charge - allowed charges are usually those where both players are making some attempt to get to the ball for a start. It's not easy to find an example, they are rare because players are not usually stupid enough to do what he did, but I've definitely seen examples before where a defender just charged a player completely off the ball, and it has resulted in a penalty. As it very obviously should. If you can't see the difference between a 'normal' shoulder barge and what this guy did yesterday, then I give up.