Ditto what Jim said.
If you are foundationless and did not move two frames up from the bottom to "seed" the top box with, then the bees were absent a guide. It's a big jump from the top of your bottom box to the top of the top box. Moving frames up allows them a ladder, so to speak, to move up. My guess is without that, they looked at all that space and adjusted the best they thought how to keep everyone together.
Shouldn't be hard to fix if you try the recommendation above.