The issue occurred in the eighth inning of a tied game Tuesday night when first base umpire Bob Davidson ruled the Indians' Jose Ramirez beat out a relay throw to prevent a double play. The replays appeared to show Ramirez was out, but the call stood after a nearly 3-minute review.
Cleveland wound up scoring the go-ahead run later in the inning.
"This is one of those rare circumstances in which the super slow motion view was delayed and the replay official reached a decision without the benefit of that information," MLB said in a statement.
Under the system adopted prior to last season, managers have the ability to challenge whether a runner is out. At that point, the umpire crew in the stadium awaits a verdict from the crews of umpires assigned to replay duty at a command center in New York.
The umpires there are supposed to have access to all camera angles from each ballpark. But it appears that the clearest angle of Tuesday night's play was not available to them.
"They admitted they missed the call. They had a breakdown in the system," Royals manager Ned Yost said, "but we had breakdowns all over the field."
Indeed, the Royals went 1 for 7 with runners in scoring position and left six on base, and second baseman Omar Infante flubbed another double-play opportunity later in the eighth that would have made the entire replay fiasco a moot point.
"I think it's a great system. There's going to be mistakes for one reason or another," Yost said. "Things happen. Mistakes are made. Just admit it, apologize for it and move on. That's what I try to do when I make a mistake."
Indians manager Terry Francona said MLB made a similar apology to him following utility man Elliot Johnson's infamous transfer play that led to a rules adjustment early last year.
In that situation, Johnson caught a deep fly ball and took a couple of steps before bracing himself against the outfield wall. As Johnson spun around and grabbed the ball from his glove, he wound up dropping it. The play was ruled a double and stood following a review.
"It was a big play in the game. We wound up losing," Francona said. "Look, I think they're trying their best to make (replay) better. I think they're doing a pretty good job of it."