Combined Hive error

Beerady lady starts with ...
I am fairly novice to keeping bees. I recently purchased two single box hives (4 weeks ago) but due to bad weather conditions had only been able to get into them today. It had been my intention upon opening that I may need to add another super to each hive as felt they may of been running out of space. In anticipation of this a few weeks ago I got out my spare boxes, waiting for the weather to be right. So today when I went to make the move I found the spare boxes FULL of bees. I feel that I may of made a mistake though as I assumed they were just my bees robbing whatever dregs were left from old colonies so continued and added the boxes to my hives. Since then there has been a lot of fighting between bees and where the “spare” boxes were there are a lot of bees milling about and looking kinda lost. I’ve since done some research and feel maybe the spare boxes had a new colony in it somehow. I’m not sure how to proceed from here, should I pull the spare boxes back off or just let them sort it out. I don’t need anyone to tell me how dumb I am as I now realize I did NOT assess the situation properly and will definitely take more care next time. Any helpful advice would be sooo appreciated.