I didn't know I had a back-up goalie either until I got the same message. Go to the HUT main screen. Select MY TEAM. Move down to highlight your goalie and then press the corresponding button for QUICK SWAP PLAYERS. It is the Y button on the XBox360, not sure what it is for Playstation 3. That should bring up your goalie and the back-up. Select the back-up goalie and press the SWAP button. This will put him in the starting position, and allow you to apply a Contract Card to him. You can keep him as your starter or use the same steps to put him in the back-up position again.
Even though the back-up goalie isn't playing in the game, he still needs a contract since he is sitting on the bench with the team. Every team has their main goalie as well as a back-up in case of injury or needing to change goalies due to a high scoring game.
