I have a very good credit score and multiple credit cards. With one card, I changed the due date to the middle of the month. On my last statement (March 8th), it said my payment was due March 28th. I scheduled a payment for March 27th. Then, another statement came March 25th and said my payment was past due and tacked me with $5.68 in finance charges. It never said that it would move up previous due dates...future due dates would be in the middle of the month. I called and they said they'd remove the finance charges. Will this go as a missed payment? Will it affect my credit rating?
Probably not. I've found that if it's something like this and you've been a good customer, they waive any late fees, probably interest, and nothing is reported. If it's Chase or Citi I say that with a high degree of certainty.
Just to be sure, you might want to call them back and ask. But my experience with them has been that unless you don't make a payment by the next due date (a month later) they won't report you. Just call and talk the them again, say it was a misunderstanding and ask if there's been any adverse reporting. My instincts say no. If they say there has been ask them if they'll remove it as a courtesy.