>if the supers are from different hives, do they ever fight?
Ever? I don't know. I've never noticed a problem. The bees in the supers during the day are mostly house bees and they don't seem to care.
>has it ever happend that you took the queen in a super?
Sure. But not often enough to consider it a big problem.
> Ten days ago I put queen excluder on top of two deeps to separate the third one which had some brood ready to hatch and some ampty spaces, and almost full shallow on top. I didn't want her to lay in that deep. She is laying where ever she founds the space. I checked the deep before, but I couldn't find her so I shook the bees off, put the excluder the deep, and than the shallow super almost full of honey. . I came from vacation, and checked on them. And gues what. All third deep was beautifuly full of brood, instead of honey. She must have been in the shallow super which I didn't check.
They are sometimes in the most unexpected places. I've found a three year old laying queen on the outside of the hive before. That was before I even opened the hive. I have also found them on the inner cover and most anywhere else you would imagine. But not very often.