Lots of factors influence this. If the temps haven't moderated yet, the broodnest is already full, and a Fall flow is happening, they are going to put it somewhere. I read recently that somebody was having a similar problem, so they added another box between the brood nest and the wet supers. As soon as that was done, the bees pulled the honey right down. Maybe they weren't ready to consolidate and backfill the broodnest, or maybe they didn't see the hive as being broken up by the inner cover.