What size of foundation are you using in the supers? If all of the other frames in the hive are drawn out and the frames that you put in the super had to be drawn, the bees may have used those as a good opportunity to build new drone comb. I use a lot of foundationless frames for honey supers and the bees build a large majority of it out as drone comb.
As far as using a honey barrier... it usually works for me, but sometimes the queen manages to find some empty comb up there. It's really not that big of a deal. Let the brood hatch out and it is likely that the bees will fill it back up with honey before the queen can find it again.
Also, if you don't want it up there it won't hurt anything to just cut it out and let the bees start building comb again. Lots of options... just pick what works best for you!