When one of my clones is facing the wrong way, it's usually because they are all in close quarters and hit a lag spike {example, running up on the Loken fight}. If that's the case, I can generally just make everyone move backwards, so the ones that were facing the right way just move away from the mob a bit. The one that was facing the wrong way now moves behind the mob and is facing the right direction again.

In wider locations, moving backwards allows me to easily see who is faced the wrong way and I can manually flip him around.