It sound's like the body control module is out of sync because the door was opened without the key being turned.

I would start by disconnecting the battery for about 5 minutes (with the key out) and see if that straightens it out. If not, maybe try doing the reverse of what you did to get here. Lock yourself in and have someone lock the door from the outside with a spare key or something like that.

The body control ECU remembers whether it locked the doors automatically, or you were the last one to lock them. It only unlocks them automatically if it gave the last lock command (I assume for security purposes), so there's some logic going on behind the scenes that is probably in a situation that wasn't anticipated and programmed for.