I'll assume that the supers have just foundation?
If so, the frames need to pushed very tight together when drawing comb. If you leave a space, they will do this. Once the comb is drawn, you can space out the frames to "take up" the 1/2 inch space that most boxes allow.
You might as well bite the bullet now and either swap out the bad frames or scrape off the bad comb. I would pull out the bad frames myself, and wait until you can place between two good drawn combs later in the season. Whatever you do, do it now! It will only get worse.