Some people were stranded for hours after major disruptions on the train network on Wednesday night.
The lack of bus replacements meant some had to fork out for hotels to stay in Wellington overnight, Greater Wellington regional councillor Ros Connelly said.
Commuter almost faints on overcrowded Wellington train carriage
A number of others from out of town stayed with friends in the city.
"And also ... just to add insult to injury, they got charged Snapper penalties because they snapped on and snapped off at the same station. So not only did their train not arrive, not only did they wait hours for a train that wasn't coming, they ended up having to stay the night in Wellington and then they got penalised for it," Connelly said.
Train services have been cancelled and delayed throughout the capital as rail staff continued their industrial action ahead of contract talks.
Initially bargaining talks were organised for next Thursday but would go ahead on Friday without the mediator.
More talks had been scheduled for Monday, with the mediator as a back-up in case a resolution had not been made.
Industrial action to disrupt Wellington trains
Rail and Maritime Transport Union organiser Todd Valster told Morning Report it was a good sign while staff were working to their agreed conditions.
"They're working to their rosters, they're working to their employment agreement, they're working to their legislation and if it falls over because they're complying to those three things, then the work's poorly arranged."
There had been seven bargaining meetings since work for a new collective agreement started in July. Industrial action was launched on Tuesday.
Wellington regional councillor Thomas Nash said the current system might need changing.
"If you've got a model that relies on workers not actually being able to take their breaks as scheduled for the model to work then that model may need to be adjusted. We're in the model that we're in for the foreseeable. So I think we do need to have a look at public transport and the rail network more generally and say 'hey, are we putting enough into this to get the right results out.'"
Fellow councillor Yadana Saw agreed the model was run too close to the bone.
"The system as it should run creates this kind of chaos, so we have a system issue here of 'is it funded enough, are the workers getting their time adequately recompensed? Are we running this as a public service?' and I don't really have certainty or assurance that that is happening."
Public transport authority Metlink said it was aware of people choosing to stay in Wellington due to cancelled trains.
It said there would be limited bus replacements for cancelled trains.
Forty services were replaced with buses, seven were cancelled and another three were delayed on Thursday.
In total, 159 services were scheduled for mornings, meaning 29 percent of Metlink's trips were replaced by buses or cancelled.