Having all of the units out of service on a platform at the same time was rare but had been an issue yesterday morning, he said.
"We don't proactively refund, because we don't know where the travel originated.
"If customers can let us know then we will certainly look at a refund."
Commuter Gareth Poley told Fairfax he was fined even though he had a valid monthly pass.
When he spoke to staff about it at the Newmarket train station he was told "you've been penalised, you should have bought a ticket".
"Had I not reported it to her they would have taken it off without me being aware of it," he said.
He planned to ask for a refund as he already paid $200 a month for his pass.