Hmmm. Well, I didn't have any trouble with that mission but I also didn't have every option enabled either. I don't know if you're right or not about an option causing a bug, but here are the options I did NOT have enabled at the time:
7 -- Credits
9 -- Research
0 -- Crafting
. (decimal point) -- Easy Level
Page Up -- Cryo
F-6 -- Easy Kill
Honestly, I haven't had any bonafide glitched missions yet though I'm starting to wonder about a couple of them that aren't complete yet. I've found the missions I thought were bugged all finally cleared when I either went back and did scans I forgot, completed some other little step I had forgotten, or completed another mission which turned out to be necessary to do before completing it.
I still have several unfinished missions so it's too soon to tell for sure. One option that's caused me some problems is the Easy Level. I finally quit using that option and just use the skills option #8 for skills. The Skills option is exactly as Caliber stated and needs to be activated BEFORE loading a save.
I've been gaming since the early DOS days, as I'm sure many here have as well, and, for me, MEA and Witcher-3 are hands down the best game with trainer experiences I've ever had. Good stuff.
[Edited by Jaks, 7/3/2017 10:10:41 AM]
My bad - I meant what was addressed with the updated trainer. 😵
[Edited by Jaks, 7/8/2017 6:33:02 AM]