The late arrival was frustrating for Janet Panabaker on Jan. 21 when her 7:03 a.m. commuter GO train from Kitchener didn't get to Union Station in Toronto until 10:17 a.m. due to bad weather.

But even more frustrating was the realization that because of the lengthy delays, the Presto fare system charged her double for the trip.

Panabaker says because she "tapped off" and scanned her payment card as she exited the train an hour later than scheduled, the system thought she had forgotten to do it earlier and that she was "tapping on" to ride the train again. That meant Presto charged her for a second $9 trip.

She says she did reach out to customer service and was told the double charge was her error.

"I really wanted to give them a chance to fix it," she said. "They're getting less polite about it ... I think that's when you start to lose patience a little bit with the whole system."

In total, Panabaker says she's incurred $45.80 in extra charges.

"I have been told that I'm going to get the money back at some point," Panabaker told CBC News, but said it's unclear when that might happen.

"I really think there's probably an awful lot of people who haven't even noticed that this happened," she said. "It's something that people need to be looking at and making sure it's not happening to them as well."

Janet Panabaker of Kitchener is warning other Presto card users to check their accounts, especially if they've experienced a lengthy delay getting to their destination. (Submitted photo)

Don't tap off after 3 hour trips

Scott Money is an adviser for media, social media and issues management at Metrolinx. He says the system is designed around the idea most of the commuter trips are at most, three hours long.

"It's designed with fare-by-distance in mind," he said. "That's why we ask you to tap on when you get on and tap off when you get off."

However, Money said "in the unlikely event a trip were to take longer than three hours," riders shouldn't tap off. Instead, check your account to see how much you've been charged for the ride and reach out to customer service if the amount is wrong.

Scott Money is an adviser for media, social media and issues management at Metrolinx. He says if riders have concerns about how much they've been charged, they should reach out to customer service. (Lorenda Reddekopp/CBC)

Riders can also set up a default trip on their card, For example, if a rider only travels the Kitchener-to-Toronto route, they can preset a default automatic charge and only need to tap on. They'll be billed the normal cost for that trip without also tapping off at the end of the trip.

"Setting that default trip can really help you avoid any kind of overcharges," Money said.

He noted it's been a particularly snowy start to the year and added they appreciate customers being patient.

"We never want to have our customers charged more than they should be."

Panabaker's also worried people who use automatic top-up for their Presto cards may not notice the double charges.

"I'm sure there are other people who haven't been checking just because that's the world we live in now. We just kind of let stuff go through automatically all the time and we don't really think about it."