Overpayment due to negligence of Manager

I am seeking some legal advice in behalf of my wife. She went on maternity leave when she gave birth to our baby. To our surprise, my wife is still receiving her monthly salary even though she should be on maternity leave status already. The thing is her Manager did not send email notifications to HR, Payroll, and department heads that's why she still received her salary for the months that she should not be getting it already. When she went back to work, she was informed that there was an overpayment on her salary and Payroll department will be deducting it from her salary. Which is obviously very inconvenient for us because half of her salary every payout is being deducted. Our question is, can we file a case against her manager for what happened? And for what grounds?

you should have informed her office nung natanggap nyo yung 1st over payment.. kung na overlooked lang talaga.. kailangan ibalik yan.. dapat hindi nyo ginastos..

Yes we know that the overpaid amount needs to be paid. However we were not able to report that incident to Payroll because at that time naka sanla po ung atm nya kaya hindi namin alam na patuloy pa rin ung pasok ng sahod nya, the thing is malaki ang nangin apekto ng kapabayaan ng kanyang manager sa sahod nya.

if you knew that it should not have been paid, then you should not have spent it, and it would be easy to just give it back.