You will have to delete the app and reload it onto your console.

Xbox 360
PlayStation 3
 

To delete the app on Xbox 360

1. Log in to the Profile that was used to download the Elite app
2. From the Xbox launch menu go to My Xbox
3. Select Game Library
4. Select Call of Duty Elite
5. Select Delete and confirm the Delete

To delete the app on PlayStation 3

1. Log in to the Profile that was used to download the Elite app
2. From the PlayStation 3 launch menu go to Game
3. Scroll down to Call of Duty Elite and Press the triangle button
4. Select Delete and Yes

Once the app is removed, enter the Multiplayer section of MW3 or Black Ops II and select Elite to download the app again.

This may also be the result of having special characters (&, ^, %, etc.) in the names of your custom classes. Removing the special characters may fix this issue.