So I was doing the 6th Alone in the Dark Quest where it sends you into the Broken Deep Lost sector for the second time to find the ghost. I had the node tracked and went into the lost sector and found out that the enemies were not aggro'ing me, gunpowder gamble wasn't gaining charges as it should, and I couldn't destroy the resonant splinters to progress the lost sector. I tried relaunching into the zone, enemies outside the lost sector behaved as usual and gunpowder gamble charged. Went back in, same issue. I went to orbit. Retried the same things, same issue. Relaunched the whole game, same issues. What ended up working was I had to untrack the quest/node before I went into the lost sector. Obviously, not a big deal and I am able to progress now, but in case someone else has this issue, that's what worked for me.