Hands up whoever here has landed on 04L in Pisa as I never have, its always 04R (the only runway with an ILS) or 22L after the circle.
And if someone wants to trawl through the piles of pointless NOTAMS for PSA (and most Italian airports) in the past, there would have been an identical NOTAM, except saying that 04R/22L is in use and 04L/22R is in use as a taxiway only as that is what I remember every time I've been there as being in the NOTAMs.
My point is is that while of course the crew 'should' have seen the NOTAM, the amount of clutter, junk, old pointless NOTAMS, etc, that a crew is bombarded with when flying to Italy meant that something being missed like this is inevitable and will happen again unless things change. The crew had probably landed 04R every other time they'd been there...throw in a controller shouting into a microphone held too close to his mouth, with a poor quality radio with associated background hum, clearing them to land and its the perfect combination.