I suspect because crossing the gap between the comb on which they were and the comb above them was something that didn't appeal very much to them whilst tightly clustered - so they stayed where they were and hoped for the best. The logic behind using deep combs is to eliminate (or reduce the number of) such gaps.
Of course there may have been other factors involved, such as colony size - a good sized cluster would probably have crossed that gap without too much hesitation. Was your colony on the small size ?
Placing filled frames in the middle of the brood chamber in the fall may cause the cluster to split in 2 when it gets cold and create more problems. You are better off making sure there are lots of filled frames above them.
Mites likely stressed the colony. Starvation killed the colony. Bees are understandably reluctant to move during cold weather. We've all seen starvation where food was a frame away. Food a box away is worse for a cold, dwindling colony that is depending on their own heat to survive. Anything that risks heat loss becomes out of the question for a cluster in trouble.
As mentioned, I'd be careful about putting honey frames in the middle of a broodnest in the fall. I'd pack the sides in and I often manipulate frames in the fall to make sure my overhead box is full.
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