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If I start a new duel and set the number of games to 3, I assume that this means play a duel which is the best of three games (ie. the first player to win two games is the winner). Except if I deliberately conceed the first two games it does not end the duel but instead invites me to start game three even though my opponent has already won the duel. Is this correct or should it end the duel after two games? I think it should be the latter.

You are correct AFAICT.

Majority vote wins!

I think the "best of" logic works for duels as it follow that used in professional play. However, for purpose of generating statistics on AI/deck strength the "play all" logic is more appropriate. The "best of" logic should only apply to interactive play, perhaps by using a new method, eg isWonOrLost, instead of the current isFinished in MagicDuel.