You just have to go along with it.
The bees in the Tardis filled up their lower hive body and then built honey comb between the tops of the frames and the lids. That can be a problem. If they get too full up, then the hive makes a new queen and they get ready to split the colony. The old queen takes a bunch of bees and they go elsewhere to start a new colony.
Beekeepers don't want that, so we watch carefully to make sure that the bees don't get honeybound and crowded. When they're almost full up, we add more supers [hive boxes] so that the bees have more room.
We have a lot of goldenrod around here and as long as we get rain, we can have a very nice autumn nectar flow, which means extra honey for the bees and for us. We added two supers of empty frames above the main hive body, crossed our fingers that the bees would prefer that to building between the layers and waited.
When we opened the hive a couple of weeks later, we found this.
Bees will do what they will do.
Even though the bees had no problem building their own comb on the foundationless frames in the lower chamber, they acted like they were totally confused with the supers.
We cut the burr comb out, explained to the bees what we wanted them to do, and then cut some old comb from a lower frame and put it in one of the upper frames. That worked. Next time we checked, they were building in the frames the way we wanted them, too.
So, my advice to new beeks is to make sure you have some sample comb in your supers so the bees get the hint. If your super frames are smaller than your brood frames, then you have a couple of options. We used the first option for the Tardis and it worked. We tried the second one in our other hive with good success.
1. You can do a simple cut out of a section of comb that's the size of your smaller frame from a bigger frame and rubber band it in place. Put it in your new super.
2. You can put a small frame at one end of the brood chamber below along side your bigger frames [second frame in from the very end] and let them fill that up. Then you put that frame into the new super. Note: They'll likely build burr comb on the bottom of the short frame, but that's easy to cut off and you can harvest it or rubber band it in another frame for them to keep using.