I heard on NPR this morning that at the time of the payments the city only had one full time employee in the payroll department and a team of contractors that didn't understand the cities payroll software. I couldn't find the article on WYPR's website, but here is a quote from Fox (I know Sinclair):

"In a response to the report, Department of Finance Director Michael Moiseyev revealed that Payroll only had one full-time employee that was supported by a team of contractors. Those contractors lacked detailed knowledge of the city's payroll configurations, according to Moiseyev's letter."