I've done the 35 prison of elders for the first time and it says you are guarteed a ship, shader and emblem and I didn't get my ship and I did it a second time and I didn't get any of those.
Yeah, I don't know. It's most likely another issue that bungie needs to work out. I beat 35 prison of elders the first time and got everything. The second time I beat it with another character and only got the ship :/