The engine Will change the player in the order of yous subs.
For exemple is your S1 is a GK, your injured player Will be replaced for the player in S2 position and the other for the one in S3 position, otherwise it Will be the S1 and S2 player that Will be put in the game.

If the cause of sub before the match is a red card and not a injured, then the engine Will replace the player with a red card by the player on the R1 position, the first player on your reserves.

This is the way the engine works, thats nothing more you can do about it.