Mortgage payment

I have a question on what I should do I have my checking account set up to make payments on my mortgage every to weeks and on the memo of the electronic payment it say extra goes to principle. Well their have been no problems for almost one year then I got a call from them today wanting to no where my payment was and informing me that I was three weeks late on it and was being charged a late payment charge. I looked it up and they received the two payments in july that should have went for my august 1st payment and appied both of them to principle and then put the payment made august 8th that should go towards my sep payment in a suspense account. The thing is I set this up a year ago and have had no problems till no and I am no sure what has happend