Major League Baseball commissioner Rob Manfred’s decision to grant immunity to players in the investigation of cheating by the Houston Astros has been one of the most controversial elements of the saga. Now, Manfred finds himself at odds with the group he made the immunity deal with: the Major League Baseball Players Association.

The Astros’ competitors—including superstars like Aaron Judge and Mike Trout—have spoken out harshly against Manfred in recent days for allowing the participants in the illegal sign-stealing scheme...