Do you have the hole in the inner cover blocked off? I think it’s recommended unless you are using it to feed the bees. If you block it off then they won’t have access to the roof space.
I just have a short round glass jar over mine. It stays in place nicely with a bit of propolis after a while and its another window into the hive without disturbing the bees too much.
I thought they might build honeycomb in the jar at some stage but mine always just stick with the Flow frames…probably because I harvest them as soon as they are full and they never run out of space,
In your case though, I wouldn’t have thought that with only 3 frames full you were too late harvesting, I’m guessing they just felt like making honeycomb in the roof because there was the open opportunity.