It would only take a few seconds, she has endured worse before. Besides, she doesnt have to phase wolverine into the ground, she can phase objects into his body.
writers must have forgotten her weakness.. i really cant comment about the twelve since i have a vague recollection.. i do remember logan stabbing her with his claws and pinning her foot to the ground
I meant she has endured worse than a couple of seconds of phasing adamantium. She has phased it and through it for longer times, like when she phased striker and herself out of synch with the earth's rotation IIRC.
She also managed to go on for an hour inside the alien breakworld metal that causes an effect similar to that of adamantium on her when she found colossus and she later phased the bullet that was made from the same material.
Like I said, she can just leave objects inside his body. Even in a featureless environment she could phase one enemy through the other and leave him there.
Kitty being vulnerable to adamantium is largely inconsistant and varies depending on the writer. She's had absolutely no problem phasing Logan in Astonishing X-Men and other more recent books.
Worst pain she has probably endured (save for the bullet) is most likely the "Kitty Proof" box she pulled the larvae from in Astonishing. It was constantly shifting in molecular structure and was way harder to get through than Adamantium.
Logan stabbing her in the foot was PIS, IMO. Especially after her being shown to not walk on solid ground in the first issue she joined the X-men. She interacts with the air molecules above the floor, as evident in the scan where Danger opens a trap door under her and she stays afloat without really having to react.