Debit order went through, im still harassed for payment

I pay my credit card via debit order, the debit order went through, I am being harassed by sms and email saying my account is overdue , by the same amount that went through on my bank account. I decide to phone in and ask, I had to hold 10 minutes for something that is clear, payment is even reflecting on account statement. And only to be told that the payment that went through was R250 short , whose problem is that? your own department saw a credit that went through on my account and decided to run a debit order for a less amount, and now you making that my own problem?