Actually, I think I know why this occurred.
When you have a huge fleet that includes many close combat, long range, and support vessels, both normal and cap ships, you can see that the formation is not only wide but also very long. If group jumping is enabled, they will maintain their formation as they prepare to jump. The rear ships in the fleet--usually the support vessels, like your Drone Hosts--will be able to jump from inside the gravity well. This could make jumps from next to an asteroid--especially a resource asteroid near the jump point--possible.
I don't think this is a glitch or possible exploit--if a player is faced with an attack by a fleet large enough that this occurs, he's got a hell of a lot more to worry about than whether a part of it jumped from inside a well.