this is a known issue since launch, for all operations / flashpoints even ilum or the fleet...
When there are too many people in one zone, a second instance of the zone is created (or a third etc..) and the people that come in are zoned into the additional instance.
The system considers it as a soft reset and all the trash from the last boss killed respawn.
This happens the other way too, at the end of the evening when your group is in the second zone and other groups are leaving the first instance, in order to save ressources, everyone is sent back to the first instance if you re-enter it and trash will also respawn.
In order to avoid being zoned into the new instance after a wipe, you must keep your current id by having one person not release their corpse and stay in the current instance until at least another person re-enters the instance and anchors it.
You just saved my guild a lot of headachs. Next HM EC we will do this.