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Sure, if the guy can't run at all he's not going to be out there. Of course, us M's fans are acutely aware of how much playing time a hurt player can get. How many months of 6+ ERA's have we had to endure before hearing, "ohh yeah, his shoulder's been bothering him the past couple of months."
Keep in mind that the manager and coaching staff are in the dugout. That can't be a great vantage point for being able to discern that your SS is running at 80%. Maybe the manager should be watching the game from the press box and relaying his decisions to his subordinates like an offensive coordinator.