SLOW trains are usually the problem but now a fast clock is creating havoc for commuters.

David Hyland, 40, has been overcharged twice after purchasing a $73 weekly myki pass at South Geelong station to travel to work in Melbourne.

He said the clock on the myki top-up machine was 15 minutes fast, so his pass was not technically active when he touched on before boarding the train.

When the call centre worker touched off at Southern Cross, he was docked $11 of myki money instead and could not use his myki pass until he paid back the $11 to get the card's balance above zero.

"I feel ripped off," Mr Hyland said.

Public Transport Victoria spokesman Adrian Darwent confirmed that the clock was incorrect and Mr Hyland's myki pass didn't work because it was purchased "in the future".

Public Transport Users Association Geelong convener Paul Westcott said he had heard of customers facing the same issue at other stations.

"It's extraordinary that you can't get an electronic clock working accurately," Mr Westcott said.

"It's just mind-boggling that this sort of thing could still be occurring with myki."

After he was initially denied a refund, Mr Hyland was overcharged again and the Public Transport Ombudsman stepped in and organised a refund.

"I'm concerned . . . I know it's happening to more people," Mr Hyland said.

"The first time I complained at the station, another person was complaining about being overcharged too."

Mr Darwent said Mr Hyland's issue appeared to be a one-off but he encouraged any other affected commuters to contact Public Transport Victoria.

He said the myki machine clock had since been corrected.

Mr Westcott warned commuters to check their balance and travel history to ensure they weren't being incorrectly charged for their travel.

tom.minear@news.com.au