That wouldn't happen if you used foundation... oops, I guess you did use foundation... ;)
Sometimes they mess it up no matter what you do, but tightly putting the frames together improves the odds that they won't do that. :)
I tend to remove the "bad" comb as quickly as I can, but yes, you can put another box on top and wait for them to move up and then put an excluder between the boxes until the brood emerges.