This is because with AutoPay there are more things happening in the background than if you just dropped a check in the mail. Everything is carefully timed so that your bill gets paid by your due date. Things can slip out of sync if you make an additional payment manually.
For instance, in this example, the customer uses AutoPay and has decided to pay an additional $3 in advance of his regularly scheduled payment. Because it takes a while for our systems to catch up to what he did, his account is debited his normal, monthly payment of $30 (instead of the adjusted amount of $27). By the following month, his accounts are in sync again and reflect the $3 advance payment. As a result, his automatic payment is only for the $27 that is due.