So I play the game with my friend on same team and when I put our motherbrain in the stage and confirm im ready, why does the game insist my friend to put motherbrain too when he confirms being ready, even when we are in the SAME team and already have one motherbrain?! Seriously I dont need two motherbrains, when we are in the same team with my friend

This bugs me too, I guess it has something to do with the fact that two players can't control the same actor.

Could be. But I remember that the earlier beta versions of Cortax Command didnt have this problem, so why does the latest beta have this problem?