Teachers have also complained that there have been issues with direct deposits not showing up, and sluggish processing of "achievement units," which are credits toward pay raises under the union contract.
At Douglass, school officials said the issue resulted from Douglass' ceasing an extended-day program this year. That extended day option in the payroll system was not turned off, officials said, resulting in teachers continuing to get stipends.
The school has an extended learning option this year, that some teachers have worked but haven't been paid for.
The district would not provide a dollar figure for how much teachers were overpaid, only saying it was "several hundred dollars" per person.
Those who were overcompensated will have to pay the money back, officials said, beginning in January.
Officials said they are "working with the principal to ensure that staff members have the opportunity to work the extended learning programs to minimize financial impact."
They also said they had communicated with the Baltimore Teachers Union about the issue. The union did not respond to a request for comment.
Officials said the district "will continue to meet with staff and take the opportunity to review compensation and address the overpayment and underpayments to ensure that all staff are compensated fairly and accurately."
In addition to paying the money back, Douglass teachers were notified that as of Nov. 6 - the day they found out about the payroll error - their annual salary would be reduced as part of a "human capital audit."