This is because with AutoPay, the payment processes swings into gear on your billing date, which is the date the bill is issued and falls 2-3 weeks before your due date. An extra payment you make may occur while your automatic payment process is already underway for the current month, so that extra payment will be applied toward your next month's bill.
Here is an example. In this instance, the customer's bill was issued on May 1. He has decided to pay an additional $3 in advance of his regularly scheduled payment on May 14, but because his automatic payment process was already underway, the extra payment did not get applied to this month. By the following month his accounts are in sync again and reflect the $3 advance payment. As a result, his automatic payment for June is $3 lower than normal.