Northwest Bank Eichelberger St, Hanover

we pay our mortgage through this bank and my fiancé stopped in to have our autopay amount changed. He dealt with Rachel and explained that we wanted to stop our current auto pay or change it to a higher amount. She had him write out a $1300 check and when I went to check our bank account, not only did they cash the $1300 but our auto pay of $1200 something was still planning on coming out. We had to call our bank to stop the payment and were charged $30 to do so. When he contacted customer service they kept him on the phone for 15 minutes just to tell him they couldn’t help. Which is why we went to our bank to do a stop payment. What was the point of writing out a $1300 check that was suppose to be applied towards our auto pay?