Is this a bug or feature?
I’d say it’s an unintentional feature. They figured that doing it that way wouldn’t cause any problems since before nox it was impossible to get more than one of the same legend. They’ll probably just make a special case for nox, since he’s the only mon causing a problem. And apparently chrono and the shiny legends don’t have the same problem since they’re still considered the same monster.
Not really a great team .even with SE 
Correct.
I have to clear this issue.
It is super rare issue and only occurs temporarily. So even you can put 2 identical monsters in a team, the system will remove one automatically later on.
Nothing to do with secret skill.
We know, but having two nox is really fun.
Using Bane and Jingledragon. (Soulstealer FL = R.I.P most of the time) 
That was what I used.
Sounds very good. I was thinking about two nox and my aurodragon at frontline. That will be 4 nox. 
lol