They way I understand it works in live is that now, since it is considered a mission item, you are only allowed one at a time. In beta you could get around this by placing your first in your cargo hold and crafting a 2nd, but now you can't remove it from your inventory.
So you can now use one Matrix Cube and one Relic, either from the light/dark vendors, received by doing Crew Missions, or if you are "Grey" you can get relics with no alignment from Flashpoints.