After repeated complaints from her, Auckland Transport yesterday refunded about $9 and promised to square up the rest of what she estimated was more than $45 in over-charges.
Another Inner Link passenger said his $1.62 fare appeared to have been transposed, to a $6.12 deduction from his card.
Matt Kyle said his new AT Hop card carrying a monthly pass was disabled when he tagged off at the end of a trip and, after putting it back in his jacket, was again tagged off as he left his bus.
He was penalised $5.04 for tagging off twice and had to add $10 to his card to reactivate his pass and get home.
"The new AT Hop system is a dog," Mr Kyle said.
"A fine for failing to tag off is offensive - their system should be robust, simple and centred on ease of use."
Auckland Transport spokesman Wally Thomas said it had identified a technical problem on both Inner Link and Outer Link routes "which may see some customers charged a penalty fare."
That was affecting about 100 passengers a day, and the council body had "a fix underway."
Mr Mr Thomas said Auckland Transport was working with the city's largest bus operator, NZ Bus, on ways of refunding or transferring balances of passengers who loaded 10-trip bus tickets on old Snapper Hop cards close to when those were replaced with AT Hop cards.
About 200 passengers were affected.
NZ Bus operations manager Shane McMahon said the company would stop selling 10-trip top-ups tomorrow, and urge passengers to run down any pre-paid travel before all its fleets were converted to AT Hop by the end of the year.