Sound to me, and please correct me if I am wrong, that when the crew is "WAY out of position in transition" that someone failed to pick up the rotation. Hey...it happens, even in experienced crews. Possibly the C picked up the Lead coming over but had a good view and stayed put to officiate the play...thus when things head the other way it looks like he/she is out of position. When either of these happen and I am the new Trail I watch the other two officials in my peripheral vision. If they correct things I just keep going. If they do not correct, I fill in as needed to get the crew back into position.
The big confusion comes when it is the T that misses the rotation of the L...because you usually end up with both busting to get to Lead. In that case, let the two of them settle and slide into the appropriate spot. It doesn't look smooth and in camp you will get "dinged" by evaluators...in real games the probability is real high that only 3 people in the entire gym will know something got messed up.