The Scot had been serving for the match in the third set when his opponent requested the umpire to review a double bounce call.
Following new protocol for the first time at the tournament, chair umpire Louise Engzell reached for a small screen to watch an instant replay of the point.
However, after a delay, Engzell told the players that her tablet was not working, and she was not able to review the call.
The US Open is piloting video review technology for the first time on selected courts at Flushing Meadows this year.
According to a document on the US Open website, the instant replays are supposed to assist chair umpires “in determining the outcome of specific judgement calls.”
However, on this occasion, it was not possible.
“It didn’t go to plan at a pretty important moment of the match, so it would be good if they could get that fixed,” Murray told reporters after the match.
While the umpire’s video screen was not working, replays of the point were shown on the big screens inside the Grandstand Stadium.
Both players, and the entire crowd, were able to watch the footage of the very tight call.
“Ladies and gentleman, unfortunately, the VR is not working,” Engzell said when addressing the stadium.
“What you are watching on the TV up here, comes from TV so the original call stands.”
CNN contacted the US Open to confirm the correct protocol was followed but has not yet received a response.
“I don’t know how exactly it’s supposed to work and who is supposed to make the decision on it. It’s quite clear from the second video that the ball bounced twice,” Murray added.
“We watched it about 10 times. It’s clearly not the umpire making that decision. I don’t know how the technology works.”
The mishap didn’t throw Murray off his game and the three-time grand slam winner was able to see out the match 6-2 7-5 6-3.
He will now face Bulgarian Grigor Dimitrov in the next round.