Thousands of city employees in Philadelphia have been overpaid because of problems with the new OnePhilly payroll system since it was launched this year, and the city is still trying to figure out how much extra cash it paid out.

About 3,800 of the city’s 30,000 employees, or 12% of the workforce, have received checks in which they were paid for hours they did not work, according to Mike Dunn, a spokesperson for Mayor Jim Kenney. The errors range from an employee who took home just one-tenth of an hour in unearned pay to a deputy commissioner at the Department of Parks and Recreation, who makes $60.75 per hour, getting credit for 100 extra hours, Dunn said. Officials hope to confirm how much workers were overpaid by the end of October, he said.

“We are currently working with departments to validate that what the system has identified as an overpayment is accurate,” Dunn said.

While much attention has been paid to workers being underpaid because of problems with OnePhilly — several municipal unions are suing over missing compensation and other issues — the city also must navigate how it will handle overpayments.

Employees will eventually be notified about how much they have been overpaid, Dunn said, and will be given two options to pay the city back: They can have it all taken out at once from their next paychecks, or they can let the city deduct an agreed-upon amount from their paychecks until their tabs are settled. The deductions must be at least $100 per check, he said. The city will ensure the overpayments do not inflate retiring workers’ pension payments, which are based in part on their final years’ salaries.

Cathy Scott, who leads the city’s union for white-collar workers, said some of her members worry they won’t have enough money on hand to pay the city back right away.

“Some of the members have expressed really serious concerns because there are significant amounts of money that they were overpaid, and to repay that is a financial strain,” said Scott, president of AFSCME District Council 47. “The OnePhilly system has created so many problems for members that trying to resolve the issues and negotiate them in a fair way has really become very difficult to do with the city.”

A $40 million information technology project launched under former Mayor Michael Nutter’s administration, OnePhilly was designed to take the city’s antiquated systems for timekeeping, payroll, pensions, and benefits and combine them into one platform. But the March rollout of the OnePhilly payroll software has led to hundreds of complaints from city workers about incorrect paychecks, missing overtime pay, and inaccurate tax withholding.

Dunn said two problems are causing the overpayments: glitches with the software that the city is working out with the vendor, and “data entry errors by administrative staff and employees themselves.”

“The goal remains to drastically reduce the instances of issues and address any that arise as quickly and effectively as possible,” Dunn said. “We are confident we will get there. In the meantime, we understand if employees lack confidence in the system, and we urge them to bring any questions or concerns about their paychecks to their departmental HR representative.”

One employee with the Department of Human Services, who requested anonymity because he wasn’t authorized to speak to the news media, described the experience of being overpaid. After noticing he was paid about $2,000 more than expected in one paycheck in April, he realized the city paid him for working 27 hours on a single holiday, when he had actually worked just two hours that day.

Worried he would get in trouble for pocketing the unearned cash, the employee notified his superiors and connected with DHS’s human resources department. He also requested a meeting to confirm he hadn’t received extra money in other checks. But six months later, that meeting hasn’t taken place, and the employee’s extra cash hasn’t been recouped.

“I wouldn’t want $2,000 pulled out of my check,” the employee said. “I have savings, but it probably would bounce my account, to be honest. I still don’t even know whether my checks are correct.... They don’t know if I’m being shorted money or being overpaid.”