Crew chief Ed Malloy said the officials should have whistled Carmelo Anthony out of bounds with about 20 seconds left and the Knicks leading 106-105.
"When we came in, we reviewed the play," Malloy said. "We did see Anthony step out of bounds and should've awarded the ball to Toronto."
Anthony had the ball in his hands near the sideline and was surrounded by three Raptors. Instead of being whistled for stepping out of bounds, he was able to pass the ball to Lance Thomas, who was subsequently fouled by Toronto.
Thomas made both free throws to give the Knicks a three-point lead with 17 seconds to play.
The Knicks improved to 4-4 with the win. Toronto fell to 5-3.
Anthony, who scored 25 points, didn't want to discuss the blown call afterward.
"I don't want to see it. I'm getting out of here," he said. "Ain't no need for me to look back and watch it. It's over with. I don't even know if I did it. Probably, but we're getting out of here with the win."
While Raptors coach Dwane Casey said he saw the Knicks star step out of bounds with his own eyes, Toronto forward DeMar DeRozan, who scored a season-high 29 points in the loss, said the Raptors still should have pulled off a victory.
"All night there were a lot of things we were definitely frustrated about," he said. "We still had a chance to pull it out. I missed a free throw, and even though I missed a free throw, we got the ball back and missed a layup. Just a combination of things."
Information from ESPN staff writer Ian Begley and The Associated Press was used in this report.