In the offseason between the 2019 World Series and whatever we want to call 2020, Major League Baseball was rocked by what has now come to be known as the sign-stealing scandal. We should loop "electronic" in there, as run-of-the-mill sign stealing has always been acceptable.
Regardless, the Astros (and later the Red Sox) were implicated for using electronic devices to decode the signs from opposing batteries (pitchers and catchers) and then using nefarious methods to pass along said signs to the hitters. For a full rundown, .
One might recall that no players were punished at all during the fallout from the scandal. Commissioner Rob Manfred and his investigative team made the decision to grant the possibly-involved players full immunity in exchange for confidential and truthful testimony.
It is a regret of Manfred's, apparently. He said as much in an interview with with Time Magazine (via The Athletic). When asked about regrets from his ongoing tenure as the commissioner of Major League Baseball, Manfred said the following:
"I'm not sure that I would have approached it with giving players immunity. Once we gave players immunity, it puts you in a box as to what exactly you were going to do in terms of punishment. I might have gone about the investigative process without that grant of immunity and see where it takes us. Starting with, I'm not going to punish anybody, maybe not my best decision ever."
The lack of player punishment has left a sour taste in the mouths of many collective fan bases and the Astros players have dealt with it in the form of boos (and more) plenty of times in the aftermath. Still, without firm punishments for any players, it's difficult to determine exactly which players knew what and that's likely the root of Manfred's regret.