One of my players got 2 yellows and was not eligible to play a league match. In the mean time i couldn’t log in and change the formation.
Then the System selected the worst player (skill wise, position wise and stamina wise) available in the squad, and consequently i lost the game.

The player substituted was from the Midfield LC position. i had 1 free player from L (passing 87), 1 young player from LR position ( passing 81 ), then another on LC (better passing than the player selected). But the player selected was from RC position ( passing 76 ). The only good skill this young player had was his speed(89).

Is this a kind of penalty or how does the system calculate a best player for any position???

There is no penalty on those situations. The best player is selected considering only the position (side is ignored) and a formula based on all skills, not only the main skills. So a player with a worse passing skill can still be considered a better midfielder if he has better secondaries.

that speed of 89 must have helped then…;)