Not sure if this is happening anywhere else, but I've just run a few space STFs and more than once I didn't receive the Rare or Proto salvage. Happened on Elite and Normal. I was collecting the salvage from my own loot bag not the optional loot.
It appears the salvage from the optional loot was being handed out properly.
A blank spot was also left in the inventory where it looks like it was going to put the item. (whatever other rewards I received in the same bag appeared after the blank spot, consoles, etc).