I'm in the same boat. Their loan processing system is very weird. If you make the part payment up to 10 days before the EMI deduction date, AND your EMI is deducted from AXIS bank SB account, you will have the problem. Strangely, if you make the part payment AFTER the EMI deduction date, OR if your payment is through post dated checks OR through ECS of another bank, you won't see the problem.
I talked to several of their employees, managers before acquiring this gyan.
I am planning to lodge a formal complaint and send it to banking ombudsman.