[MD] Payroll MESS: Agency I Work for Wants Me to Pay Them Back?

I am a city employee in the state of Maryland under a special type of contingency worker contract that does not provide benefits or paid time off (including holidays). My wage is hourly, and I clock-in when I get to the office and I clock-out when I leave using one of those standard cloud-based HR and finance softwares (like ADP).

For the past year, I have been requesting time off by selecting the code "permission time-off" selection in my account's timesheet. It then goes to my manager for approval which she has been approving. Apparently my manager was NOT supposed to be doing that. The code I've been using is apparently only to be used when city offices are closed in lieu of special events like a snowstorm for example. We both had no idea that this code was off-limits and its created a mess for me. According to my manager, HR is supposed to be contacting me soon, and from what my manager has gathered, it sounds like they want me to pay the agency back for the hours I used that code!?! Apparently I was being paid using that code during my time-off?? They have not contacted me yet.

I know I don't pay attention to my paystubs as much as I should, but my paychecks fluctuate so much already, so I haven't noticed any substantial difference. Do you have any advice or recommendations on how I should handle this? How to best advocate for myself? I was going to file my taxes this weekend, but because of this, I'll need a new W-2 in-order to do so by April 15. I'm really upset, confused and pretty disheartened. I'll be leaving this job before the fall thankfully.