It's not skipping completely per say. From what I've noticed, depending on your initiative and how close in proximity you are to a certain member, you both go at the same time. The bug(?) here seems to be that when you hit End Turn on one member, it ends it for both EVEN if you haven't done anything on the other character. There really should be a warning when that is happening OR make End turn not end all members turns.
That definitely seems to be a part of it. Most of the time this has happened, they've been right next to each other in the turn order. Though, there was one instance where an enemy had their turn between ours, and it still seemed to skip my companion's turn. It's possible that that enemy applied some sort of effect causing my companion to lose her turn. Even if a character can't do anything, it might be good to have it still stop on their turn as a reminder of the effect.