Strange bee behaviour

It's been a week since I carried out swarm control. My method proved to be controversial on twitter as all the tweeting beekeepers I spoke to (apart from fellow Beehaus owner @willipmrpip) said that I had done it wrong. I had taken the queen and the brood to the other side of the Beehaus (effectively it's a Dartington with an entrance either end and a dividing board in the middle) and left the flying bees with the queen cells. The method that most use separate the queen and flying bees from the brood and queen cell.

The next day (following my previous post below) I did try and rectify my mistake by attempting to find the queen and move her back to the flying bees. But I couldn't find her and the bees were getting more upset after my second attempt at going through the frames. So, I just closed that side up. Having spoken to @willipmrpip on twitter, he informed me that this method had worked for him so I decided to leave it and next time I carry out artificial swarm control, I'll do the popular method.

Then on Sunday, I went back into the 'flying bees and queen cell side' to remove all other queen cells apart from one, which I did. On the one frame they had made loads of emergency cells but I left one of the original ones that looked long, acorn shaped and capped over. Hope I left a good one.

I was walking back towards the house when I noticed a number of bees nosing around the bait hive (the nucleus box I bought my first colony in) that I'd balanced in the tree. You can see the set-up above. I just thought these bees were being curious.

My husband noticed the same when he was mowing the lawn yesterday. Then yesterday afternoon there was an enormous amount of bees buzzing around this box. Not a mass as in a swarm but definitely loads. It went on for 10 minutes or so and then settled down. I thought they'd all just gone back into the Beehaus.

This morning, as I noticed more bees near the tree, I decided to take this balanced box down to see exactly what was going on inside and this is what I was greeted by (I had put an old frame in there to may it smell like bees):

Only expecting a few bees, I was shocked to see so many inside 

They have even started building foundation

I closed up and put it back in the tree as not entirely sure what to do

So, what's going on? Who are these bees? The swarm ones who would have swarmed with the queen? On the one end of the Beehaus I have a queen who can't fly and on the other a queen cell with no queen. And bees are still going in both entrances. Would bees congregate in a box with no queen or are the waiting for the queen to hatch and then bring her to the box? Also, they can't stay as the box is literally balanced in the tree and it's not water tight.

It's all very odd and I'd love some enlightenment to all these questions!