The watchdog received 12 complaints after a string of Bluebridge failings in February and March last year - one from Consumer NZ and the rest from passengers.
StraitNZ Bluebridge's fine print claimed the company was not liable for delays or cancellations - even when they were within its control.
But the commission's fair trading general manager, Vanessa Horne, said the clause was likely a breach of the Fair Trading Act as it misled consumers of their potential rights under the Consumer Guarantees Act.
"Their terms and conditions said that they weren't going to give customers compensation. Actually, what we found out when we did our investigation, is that they did compensate consumers.
"While in practice it looks like they were doing the right thing and refunding their customers, their terms and conditions were inaccurate.
"The reason why that's really important is that some customers may have read those terms and conditions and decided that they weren't going to pursue compensation."
About 340 customers approached Bluebridge for refunds related to that period and those claims had been considered, Horne said.
She advised anyone who thought they may have been entitled to compensation to contact the company directly.
The commission was pleased with the work Bluebridge had done "behind the scenes" since the regulatory authority began investigating last year, but had issued the warning as a reminder to other companies.
"This type of thing is not great practice," Horne said.
"A warning recognises that there is some room for improvement, but that consumer harm's been addressed with good practices by the businesses themselves.
"They've obviously updated their terms and conditions so that they do comply with the law, but also they've reviewed all of their processes, they've got new workflows for refund requests they've put through, and they've trained their staff as well on all those procedures.
"In other circumstances we would be looking to take enforcement action through the courts, but in this situation we think Bluebridge have done a good job of recognising our concerns and customer concerns."
The commission's findings come just days after yet another technical failing on the ferry line. A passenger said people were plunged into darkness when a ship briefly lost power coming into Wellington Harbour on Saturday afternoon.
RNZ has approached StraitNZ Bluebridge for comment.
