I had issues with injuries as well. For some reason, you can not take them off the DL....even in the editor. The game will not change it. I messed my franchise up by doing it and it crashed everytime I tried to play because a team had too many players and I could not repair it. I had to start over. So now I do not mess with injuries. The only solution is to wait it out an turn off injuries.
maybe someone else here has had better luck fixing it.