John Terry attempted to clear the ball from the under the bar following a shot from Marko Devic, but television replays showed that the effort had crossed the goal line.
Collina blamed human error for the wrong call, but insisted that the other two similar situations - in the group matches between Germany and Portugal and Italy and Croatia - were handled correctly.
|More goal-line drama for England
The incident has reignited the debate over whether the introduction of five officials actually helps to prevent bad calls from being made.
"This is the only problem we have had," Collina noted.
"It is one negative decision in three years of Champions League and two years of Europa League and 24 matches at the Euros.
"I would be very happy to know if the same questions would have been asked without yesterday's decision."
After the match, Fifa president Sepp Blatter wrote on Twitter that the introduction of goal-line technology "is no longer an alternative but a necessity".