I have no idea what you mean. You have a hive body (deep box) on top of the inner cover? Does it have frames in it? Was it there as a feeder? Why is is there?
If you put a deep on the inner cover the bees will find any space more than 3/8" and fill it with comb. So of course, if they have access to that box and they need the room they will fill it with comb.
Is it full of honey? Brood? Where's the brood nest?
I find it to be pretty normal to have from a few to a lot of bees on top of the inner cover if you have the top propped up a little for ventilation. I had a lot of bees there all winter in several hives. I think the heat coming through the hole in the inner cover keeps it warm.
In summer, I have less there, but there always seems to be a few. I always thought that it had to do with temperature control. Like bearding in the summer. Some will move up on top of the inner cover.
OK. I've read this several times and maybe I'm just missing the idea that there is just an inner cover and it has bees in it. There are usually bees in the inner cover space if it's warm. They keep the ants out.
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