As a result, the results had to be counted back to lap 68 rather than the scheduled 70.
"There are no models as marshals or stewards either are there?" joked Force India sporting boss Otmar Szafnauer.
Harlow said she was simply told by a race official to wave the flag when she did, while the FIA's Whiting confirmed that it was "a communication error".
"She was given the order too early. So it's not her fault," he is quoted by Auto Motor und Sport as saying.
The actual mistake was apparently made by a local Montreal official.
"He asked the race director if the race was on the last lap. But they understood it not as a question but as a statement and answered ok," Whiting said.
Whiting added that it was a serious mistake, but also defended those who made it.
"Wherever there are people, there will be mistakes. We have different communication systems and different languages at every track," he explained.
"We could think about replacing the flag with a signal on the LED boards. But it would be a huge hassle for a problem that occurs once in a decade."
The actual result was not affected by the mistake, but race winner Sebastian Vettel admitted that it is a problem.
"I was just worried," said the Ferrari driver. "I told them on the radio that people should not jump on the track waving and celebrating, because we're still at full pace."
The championship continues with the French Grand Prix next weekend.