AS MENTIONED MULTIPLE TIMES, THERE ARE SCRIPTED EVENTS IN THIS GAME THAT WILL NOT WORK WITH CERTAIN TRAINER OPTIONS ON. THE GAME EXPECTS CERTAIN THINGS TO HAPPEN THAT ARE NOT POSSIBLE WITH THE TRAINER IN USE. DISABLE THE TRAINER FOR THESE SECTIONS OF THE GAME.
If you want to request additional trainer options, you can do that here: Link
[Edited by PWizard, 10/12/2017 4:28:13 AM]
If it is helpful, I can confirm that using the Steam trainer it seems to be only the Health and Easy Captain Kills options that are problematic in those scripted events. I managed a complete playthrough keeping on Stealth, Unlimited Arrows, Unlimited Focus, Unlimited Wrath/Elven Rage, and Unlimited Might the entire time without incident.