Here's 2 examples that have happened at my work.
1. payroll person flip flopped account numbers of 2 employees causing them to get each others paychecks. Money in their accounts gets frozen, removed, they get cut live checks for the correct amount instead.
2. payroll person fat fingers an hours column causing an employee to be paid 12k instead of $1,200 Money in their accounts gets frozen, removed.
What I assume to be true in this situation is that this isn't the first time it went to your account. That that is the way it often was and now that you are longer together she put in / should have put in for the change. Unfortunately money in your account doesn't make it your money.
Girlfriends may as well be in the category of family as far is if you loan it money do so being ok to never see it again.