I think you are confusing real life with BB. In real life a player in top shape is less likely to be injured than one that is out of shape unfit and already carying niggling injuries. But they can still happen to anyone.
In BB the only things that affect the chance and severity of injuries and the aggressiveness of your player and the aggressiveness of the player he is playing against. You can get a rough estimate of this by looking at the foul average of the player. Bad defence also causes more fouls so it can be tricky to judge opponents but if they get a very high match rating but lots of fouls, then they are aggressive.
Once it is determined by the GE that an injury has occured the final factor is the teams doctor.