The note and security instrument usually will list the order of application of payments.  The order is usually first money to interest, then to principal, then to escrow or advanced funds and finally to late charges.  You should review the application of payment section in your note and security instrument [mortgage deed or deed of trust] and if the payments are being shorted, you should point this out to your lender.  You will want to address this with your lender immediately, because if they are reporting wrong information to the credit bureaus that will be time consuming to fix and may affect your credit in the interim.  You will still need to pay the late charges at some point in time, however.

If the note and security instrument show that the lender is applying your payments incorrectly and refuse to correct the information, you should contact either an attorney or your state's banking department for redress.  But, you should always give them the chance to correct the problem.  And you should calmly cite the section in the note which addresses application of payments.  Talk to as many supervisors as you need to and have them issue you a correct statement.