I've had this couple of times, and i think i know how it happens: My fleet was in phase jump, when i issued it a new destination, after that, the ships ignored group jump command. It has happened to me twice like this, but someone else should try to reproduce it.
I can confirm this behavior, but sometimes it doesn't update their target while they're not in phase jump
Additionally, I've had a large chunk of ships waiting at the edge of the gravwell, and then two or three ships will just jump.
My hunch for this latter case is that despite being in a group, they're not all in the same fleet. Maybe I'm just not using fleets right, but it seems that if a ship doesn't auto-join, then i have to recreate the fleet entirely to get it to join.
I'd expect the grouping behavior to occur based on who you issue the orders to, not based on fleets.