EMI's paid on time but Bank saying that I defaulted on payments

Hi There, I have taken a loan from HDFC bank in year 2015, the tenure of loan was 24 months and EMI was auto debited from my salary account; however after 3 months my employer changed salary account from HDFC to Kotak Mahindra bank. I informed the same to HDFC bank customer care and asked them to change my bank details for auto debit of loan amount every month; however none of their team members did the needful and i kept on depositing the monthly EMI through online banking (manually). The last EMI paid to Bank was on 07/12/2016 and loan was completely paid in time; however now i got a call from HDFC bank regarding the bounce charges applied on the 21 EMI's which got bounced due to insufficient funds. I told them the entire scenario and asked them to wave-off the charges as i have already paid the entire loan amount. But they are now threatening me to go legal. Kindly suggest me the legal options i can opt. Regards