Bad writing, Carbonadium from what I know only slows Wolverines healing factor it can't cut through adamantium. So really it's just PIS take it how it is Marvel writers tend to forget things and power up other things. Good example of that is Ultimate comics Ultimatum where Wolverine is killed in that universe but his healing factor is much better than 616 Wolverine's as if one cell remains of him he can regen, but in that comic they forgot about that since his hand was still remaining which means he should have recovered.
You're right, if Carbondanium could kill him then Omega Red would have killed Wolvie in the 90's, and again in origins.
Now unless Doom flies in on Space Punisher's back shouting campy 70's phrases, I don't know if I can follow the first FF anymore. The second FF just looks dumb, She-Hulk and Ant-man are the only positives, a C-list Inhuman and half a Thing are just mediocre.
Gotta say Fraction taking over FF is a catastrophe, but he had to ruin another book so why not?