The MTA is still working out some kinks in its new OMNY tap-to-pay system, which will be the only way to pay for subway and bus trips in New York City when the MTA retires the MetroCard at the end of this year.

Riders have highlighted several issues with the new technology in recent months, such as temporarily being charged multiple fares for a single trip and being unable to determine when they qualify for free rides through the MTA’s “fare capping” policy that limits how much riders are charged every week.

The MTA initially planned to retire the MetroCard by the end of 2023, but issues with the OMNY rollout pushed that deadline back by two years. The entire transition began in 2017, and has taken more than eight years to finish.

MTA officials said the technology is finally ready for prime time, and noted earlier this month that 94% of all transit trips in the city were paid for with OMNY. The agency touts OMNY as a boon for riders that allows them the flexibility of paying with their smartphone, credit card or special reloadable OMNY card.

“Our riders have chosen to use OMNY instead of a MetroCard — not once, or twice, but 3 billion times,” MTA Spokesperson Michael Cortez wrote in a statement. “We've given them a better way to enter the system, and they've taken it. That's the story of this transition.”

But surveys from transit advocacy groups earlier this year found not everyone is enamored of the new system. The group Riders Alliance said straphangers reported being locked out of the system after they tried to tap a commuter benefits card that had run out of money — and they remained locked out even after they were reloaded.

Other riders said they’ve haven't been able to reload their OMNY cards at all.

OMNY readers are easier to use than the MetroCard swipe slots. But some riders feel the new system isn't as reliable.

In October, Brooklyn commuter Ilene Rosen got an email that her OMNY card could not be reloaded online. After failing on three different days to connect with a person on the MTA’s customer service hotline, she opted to try to the MTA customer service center at Atlantic Terminal.

She said she was unable to fix the issue at the center — but managed to add $100 to her card at an OMNY vending machine in the subway.

“I would think, considering the MTA is disappearing the MetroCard at the end of the year, OMNY is not ready for increased use of their system,” said Rosen. “They don’t seem prepared to deal with a massive influx of passengers.”

A leading issue flagged among riders was that they didn’t know how much the MTA charges them every month. The MTA board mandates that if a rider pays 12 fares in less than seven days, any remaining trip they take that week is free. MTA representatives said the system adheres to that policy, but riders noted it’s confusing and could be better communicated.

MTA Chief Customer Service Officer Shanifah Rieara acknowledged that demand during a board meeting earlier this month, and said the agency was working to eventually add a function that lets OMNY users know how close they are to scoring free rides.

“ Those are sort of improvements that will be coming in the near future,” she said. “We are constantly meeting to get this right and meeting with the vendor to ensure that these features and functions are in place for customer reassurance and credibility.”

Some riders also noted that when they pay with their iPhones, their fares sometimes take several minutes to post to their Apple Pay accounts. Katherine Mendoza said that got her in trouble when she ran into the MTA’s EAGLE team on the M15 bus in Lower Manhattan over the summer. The officers use special devices to check whether someone paid the fare and Mendoza said it showed she hadn’t paid.

She said she thought it was a one-off, but then it happened again. That time, she said she showed the EAGLE team her phone, which stated her fare payment was still pending. She said the officers issued her a $100 fare evasion ticket anyway.

“ I kind of like gaslit myself,” said Mendoza, 37. “ I know that might sound like an isolated incident, but something's wrong."

MTA officials said they've opened 30 new customer service centers to help riders transition to OMNY, and has held more than 100 outreach events on the new technology at senior centers, hospitals and houses of worship. They said they’ll deploy extra customer service representatives to subway stations at the start of the year to help the final MetroCard holdouts make the transition.