His compound clip is included the whole gap clip to the left of the transition. I'm trying to duplicate, and mine only takes in the transition, but not the whole clip before the transition. So yes, I see a discrepancy here. Not sure what's going on. No known bugs for this to my knowledge.
So I've isolated the problem. It was only occurring after a certain point in the project. Everything before it would group properly. I had some connected clips grouped above a gap clip , and the issue disappeared once I moved those to the primary storyline. Very strange.