Bees being bees! 
Think about it - in nature, bees find an empty hollow space and start at the top, building their combs downwards from there. If you put them into too much hive space, they will start at the top.
Inspect the inner cover - they probably built comb on it. I would carefully cut it off the inner cover and rubber band it to empty frames. Shake any remaining bees off the inner cover into the lower box with 8 frames in it. Take the empty box away completely. Leave them for another week or two and inspect again. 
Here is an example of rubber banding in case you haven’t heard of it before: