With patch 4.1 the functionality of graveyards within the Battle for Gilneas was changed.
Players who die at a control point that they own will now be teleported to the next closest graveyard, instead of the one at which they died.
If a player's team owns the Mine and Waterworks, and dies at Waterworks, they will be teleported to the Mine.
If an Alliance player's team only owns Lighthouse, and dies at Lighthouse, they will respawn at their base.
If a Horde player's team owns Waterworks and Mine, and dies at Lighthouse, they will respawn at Waterworks.
In summary, when a player dies at a point that the player's team currently controls they will not resurrect at that point's graveyard; rather they will resurrect at the next closest controlled point or at their team's starting location if no other base is controlled. This behaviour is counter-intuitive to many players and is often incorrectly reported as a bug.