Bee will do what they want ! From your comment I surmise that you went natural foundation less frame wise. Even with foundation bees can build odd side n/or burr comb.
There are people of both conviction on this forum but I tend to warn newbees to strain/stay away form the foundation less setup if you can’t be in there watching continuously. In the 1950’s n 60’s we was a youthful young buck n all we used was wax or reenforced wax foundation.
That said, you’ve experienced why I have stayed away from a empty frame approach. But it’s too late for you at this moment ! Let’s make the most out of your mess ! It’s not all a loss. We do learn most from personal experiences. Now try to clean up the worse of the worse n add to a used wax pail for later use. The natural comb that seems less out of control careful guide into the frames … LARGE rubber bands are helpful foe securing larger pieces of comb into empty frame. Do the best you can. Ain’t beekeeping fun yet.
It you do want to use some foundation less … Alternate an empty with a frame that has reenforced wax or waxed plastic foundation … Note: don’t do that with brood at this time. Your still learning ! Actually we all are learning. My ’s are always tossing a new twist at me !
Next time pop a couple pix’s at us. It does help to give more accurate answers …
Cheers n good luck.
PS … Others should pop in here with thots, experiences n ideas too