Am I financially liable if the bank made a mistake on my account and I withdrew more money? How?

My child's father deposited a check in my bank account without me knowing the amount. When I checked my bank balance it told me that I had $1083.00 in the account. I withdrew $950 in person at the local branch to pay rent. Then the bank advised me that the check got deposited twice and that I only had $540 available. Now they are trying to tell me that I owe them $406 for their mistake. Am I financially liable?