Yep, I've had the same problem. In particular, the Return to Yankee Station and Okinawa scenarios. It also happens a lot when I have amended a scenario in SE and then play it in regular mode...all my default settings have changed, and sometimes the game will attack blue vampires. I've noticed another strange behavior in these scenarios also...when I really unload on a red surface group, for some reason just before the missiles hit home, the surface group starts launching torpedoes in addition to their point defenses. I don't know WHAT the heck that's all about or what causes it. More than once, playing on EASY to see maybe why this is happening, red side has sunk their own submarine, although this may be happening because of the dice roll and the AI is having trouble with their detections. And finally, I'm getting messages from air groups on AAW missions just before they bingo out and head for home, that the air group has no orders. Then they instantly disband the group and head home individually, which is normal behavior. In previous versions I got no such 'no orders' message.
This is not a priority 1 issue but it's a little annoying.
You might check your formation editor and see if this behavior stops if you remove all aircraft from the formation and handle your BG pickets and screens manually.