Bethesda can't even keep consistency between its own games, or even one game, for that matter.
In Fallout 4, it is stated that all mutants in the Commonwealth are created by the Institute. That means complete isolation in an underground lab; the mutants would never be able to return to it. Yet their numbers keep increasing, even though the FEV experiments were shut down, and super mutants keep kidnapping the people they don't kill and can often be heard looking for 'the green stuff', suggesting they're reproducing on their own.
Which is impossible.
Additionally, and this is sort of a spoiler, during the main quest you meet a mutant named Virgil (which, in a feat of amazingly lazy writing, is his actual surname) who was once a revered Institute scientist but escaped by turning himself into a mutant. He then tasks you with grabbing him the cure for FEV exposure he believes to have been inside the Institute when he escaped, which is stupid on several levels. Firstly, he's not SAFE from the Insitute now; why is he turning back? Is the fact that his cave is radiation-free not an oversight by the programmers? Then why turn into a mutant at all, why not just grab a hazmat suit? The risks of turning into a mutant were so incredibly high (first and foremost, forgetting his own goddamn plan along with his identity) it wasn't worth it in the slightest; only through sheer luck did he remain fully cognizant.
Secondly, how does the cure even work? The FEV is a virus, yes, but its effects aren't symptoms; it modifies DNA to what it 'thinks' is perfection. It could, of course, be another modified strain that recreates his original DNA, but it is specified to be a cure he didn't create that works on ALL FEV-affected subjects. Not to mention that A. IT WORKS, and B. It shrinks him, which I can't imagine would work without some sort of shedding of various extra tissues and bones.
There are way too many ghouls, as previously mentioned, and not only that but they also just seem to be either deformed or burn victims. Feral ghouls and normal ghouls look nothing alike and neither of them are really walking corpses like they're meant to be; they're not rotting or anything.
I have more complaints, but I'm pressed for time.