I guess you had a really bad player on your team
Sometime even in "equal" teams - one of them (in one round) playing just perfect, while other doing nothing.
In this case also appear this warning message.
Had this happen last night in a siege battle. We had 2 really good players and the enemy had a balance of good players, we still defended our castle yet the teams were not fair enough to justify a multi. Oh and nobody got "autobalanced" either after the round. It was around 50 vs 50 as well.IMHO it was because of "weight" of each player calculating in "long run". I.e. 1-2 excellent round played by some players does not really affect their "weight" for balance system.