First rule of FM, never make any kind of unforced substitution, let alone a defensive one, when you're trying to hang on to a lead! It just gives the ME an excuse to let the AI team score! I've kept players on the pitch at 50% rather than sub them 'cause I know exactly what would happen!
Are you serious? I've always tended to sub guys off if they've dipped below 70% and are not playing very well.