There is a few issues I have noticed as well. 1.If you snipe from the ship after the first wave is complete you will have to go back to the door and restart it again ( it can be a good thing if you want to farm glimmer) 2.also the first part of the mission once you clear the hydra and you go on to the next part there was only a captain. I did not read your whole post sorry so I don't know if you mentioned these things.