You absolutely can't allow them to do that. It has to be removed. The frames need to be close together which doesn't stop that from happening but it lessons it. If you wax the frames, they should build the comb properly. You should also wax the bare spots on the ones that have gone wrong in order to insure that the entire frame has a small coat of wax and re-educate them.
I'm thinking you maybe shouldn't have honey supers on yet. It depends how many frames are drawn in your brood boxes. I suspect they don't want to go through the queen excluder and the empty super to get to the feeder.
As for the queen issue, I'd like to come and see the hives. We want to make the best of a difficult situation. No sense in letting them fade away. One option is going to be to combine the weak hive with the strong one using the newspaper method. I'll contact you outside of this forum to arrange a time.
Thanks for writing to the forum. There are lots of folks with issues and we'll learn from each other.
In the latest news, I added the supers with a queen excluder to my 2 hives. Since this addition, the bees have not gone up to the feeder box. There are usually a couple hundred bees in the feeders when I check. Today there were zero.
Another possible issue... the bees seem to be building the comb out sideways from the frames instead of along the frames. This is connecting frames together in the center. See picture.
I'm leaning towards letting the queens do or die. I see this as a big experiment since it's my first year with bees. If I'm crazy, please tell me so. If you feel like I really should replace the queens I will.