I use foundationless and every once in a while you will get a hive that doesnt follow the cad drawings Make sure your hive is near level in both directions, a slight slant to front or back will help with drainage but dont make it a bunch.
If you have a spare box, just suit up and go in that box and start gently removing what you have too to pull frames is what I'd do. Use the extra box to hold the cleaned up frames as you go so you dont have to tackle the full weight of the brood box. Good idea to have a clean bucket with a lid to keep any clean honey comb you have to remove as well. From the couple times I've had hives like this, it usually doesn't fix itself and just gets worse if you dont act.
Also helps to pull a couple drawn frames up into a new box to give the bees a reference guide for drawing combs next to them.
Last, most of my hives will have a "bridge" between combs , usually near, or attached to the top wood of the frame, most times it looks worse than it actually is.
Sounds like you may be ready for honey super.
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