Sometimes I get a random object in a different layer that overlaps that gets it confused. I go into illustrator, laso all the objects in that area, then check the layer hierarchy to see if something was selected in a different layer than I expected.
Other than that, as you say, go through each object in the hierarchy inside CH and see if there are any unexpected pins in other groups. Sometimes I drop a draggable somewhere by misclick in a nested group that I did not realize. I don’t know a better way than going through each object one by one in the hierarchy tree and checking each one.
Sometimes when this happens to me, it isn't only the pins/layer independence that causes this kind of warp, but also the attach style in the Properties Panel is sometimes set to "hinge" or "weld" instead of "free." The most important thing to remember about Ch that I've learned is that even if a layer is not independent, sometimes it needs to be independent capable to function correctly. (So your character's shirt could be set up as independent with free attach style, but then set it's independence to false, or else it won't move correctly with the walk behavior.)
Hope it helps!
Thanks. That's really interesting and could be the answer to so many small and large issues. I'll try that out tomorrow.