ECS Was Done After Making Payment

My name is Praveen, I have recently taken personal loan from a bank. I have taken a personal loan in September and my first EMI was on 5th October, but the EMI was not deducted as the ECS was not activated, I got emails from the bank to register the eMandate again and I called the helpline number to double check and registered the eMandate again as advised by the phone banking representative. Also, I got calls from the recovery team to make the payment manually using billdesk and I did the same on 15th October and gave the payment reference number to the recovery team. On the same day(15th October) again ECS debit was done in my account and it was returned due to insufficient funds. It's causing a negative impact on my account and I was also charged by my bank because of ECS return. I was calling phone banking regularly to check how I can make payment and did the payment as advised by the phone banking representatives and recovery team. Can I complain on the bank as its a mistake by them