The bizarre sequence started with Baltimore leading 2-1 in the top of the third. Nick Markakis was on third base and Miguel Tejada on first with one out when Ramon Hernandez hit a line drive to center field.
Indians outfielder Grady Sizemore made a diving catch. Markakis tagged up, headed for home and appeared to cross the plate before Tejada doubled off first. Plate umpire Marvin Hudson waved off the run.
Orioles bench coach Tom Trebelhorn disputed Hudson's call before the start of the fourth, and Hudson then conferred with Montague and the other umpires.
"We kicked it around and now I'm having a brain cramp on it," Montague said. "So I sent Bill (umpire Bill Miller) in, I said 'You know what, cause we're debating, you go in. Lets make it 100 percent sure."'
Miller checked the rule and said the run should have counted. Montague was vague about why it took until the sixth to make the change, saying "it kind of went on" with the umpires conferring with the managers.
"It was my screw up and we can't go off of umpire's error," he said. "What's right is right. We have to score the run."
Montague said he couldn't remember anything like it happening and didn't blame Wedge for his protest, which will be decided by commissioner Bud Selig's office.
Wedge protested the game because the change was not made immediately.
"I know the umpires have a tough job to do, but there is a process and there are rules," he said. "When the next pitch is thrown, that's it. The fact is the home plate umpire waved it off. I've never seen runs put on the board three or four innings later."
Baltimore manager Sam Perlozzo said Trebelhorn alerted him that the run should count.