Weird. I'm on my 3rd play-through (going for 100% this time) and I have yet to have this quest, or pretty much any quest, bugged at all, and I've used the trainer throughout all of it. I wonder why that happened to you.The only quest I've had bugged was the Nomad shield crafting quest, but even that works, it just doesn't get rid of the item in the Development tab.
My experience has been much the same as yours. I just finished the main story and used the trainer a lot the entire time. All my system scans are 100%, my Heleus overall is at 97% and my game progress is at 97% also. I have 2 missions not finished, one I think I'll complete and one I'm not so sure. Ryder Family Secrets and the Data Cores.
For me two things affected my progress more than anything. When I got stuck on a mission, I could leave a planet and go do something else then when I returned many missions picked right up again. The other was scanning. There were a lot of times a scan of something not yet scanned kicked things in gear and I was able to proceed again normally.
There are a lot of quirky things, too. Like the Architect that could glitch out if you went after him with your most powerful attacks. Come to find out the way to beat him was to gradually hit a leg to about 50%, then same with the head and be sure to let the Remnants spawn. Did that with all three legs and finished him. Saw it explained at answers.ea.com and it worked perfectly.
While I can appreciate the Devs leaving things for us to figure out, there were lots of times when I cussed them up and down for not having any visible mission progress markers showing. I wasted a ton of time with some of those.
[Edited by Jaks, 7/10/2017 5:40:21 AM]
What missions get stuck for example while using which options? I might play thru again and could try them out here. They have to be easily reproducible so Caliber can see them doing it as well otherwise he can't fix anything.
You have to consider multiple people are using the trainer that are also reporting having completed the game and most all missions.
I've had a little issue with 3 options but none that glitched my missions. The Easy Level as has been reported before. The / Radiation and Life Support which spazzes out sometimes. Cant have it on while in Nomad but should have it on outside of Nomad. And the F7 Buddy Protection. My squad mates still go down and have to be revived. But none of those have glitched missions for me that I can tell.
Also, keep in mind there are 6 options that the Readme says to turn off when not needed. I agree with Loki, it's the game itself causing problems. Every mission I had some kind of problem with has volumes of text and lots of people reporting them, all looking for answers and work-arounds on Google and You Tube.
[Edited by Jaks, 7/10/2017 8:11:38 PM]