I know this quest can be done because I've completed it normally. I've also completed it and had the same problem.
Thing is, there are a LOT of quests that are horribly bugged and can be completely broken and unable to be completed if you do them the wrong way.
There's a late-game mission, forget the name. Where you have to track down leads from an old salarian STG guy. One lead ends up on Elaadin where he crashed? Anyway, you have to track him from the crash to a nearby raider camp. Problem is, the game spawns the raider camp (without the salarian) before you get to the crashed ship. I cleared out the raiders on my way there and then the crashed ship wanted me to track the salarian back to the raider camp... which was now empty. Mission ended up stuck and unable to complete. Had to re-load an older save. Second time through, I ignored the raider camp, went straight to the ship, tracked him back to the raiders, cleared them out, and rescued the salarian, completing sucessfully.
A LOT of quests are like that. Same thing with the kett base. You have to do things in the proper order or the quest journal entry bugs out and gets stuck forever.
Some quests, I still haven't figured out the right order and to this day have never finished them.
One such quest is EOS' "Naming the Dead". If you drive past a place that has a body, the body will spawn and de-spawn, never to re-appear so you can't scan it to complete the quest. I've never actually been able to complete that one.
Then there are all the quests where you have to find something in a kett camp, usually 3-5 things in different camps. Eventually they all stop working. I've never been able to complete any of those. I always end up with 6 or 7 of those quests stuck in my journal unable to complete them.
Unfortunately, the game has a LOT of bugs and it will NEVER be fixed because it was completely abandoned. No hope for a "remaster" either.