I was having this same problem where they just mopped the floor with me on veteran difficulty so I switched it down to story. That didn't change anything at first as I continued to get badly beat. So when I was back at the med center I ended up waiting there while I read this thread. By the time when I went back into the story section all enemies reset and the two bosses were both on Story difficulty. Waiting just 5-10 min outside the zone reset it and all enemies were on proper difficulty. Hope this helps!