I just don't understand why Noah Vosen's whole team didn't pick Jason's "di Piento's" passport in The Bourne Supremacy when he arrived in New York as they should have known all Jason's identities but Landy's colleague picked it up.
This is actually explained in the scene. Vosen is clearly relying far too heavily on the information from "The Grid" (e.g. a series of flagged passports and identities that have been loaded onto their fancy CIA computer system regarding all of Jason Bourne's previously used aliases).
We learn, however, that the di Piento passport has never been used and hence isn't on the watchlist of identities that Vosen's people are looking out for.
Cronin: A passport for Gilberto di Piento has just cleared immigration. It's an early Treadstone identity registered to Jason Bourne. But he never used it and it never went to the Grid... Bourne's alive...
As to why Landy's team have it and Vosen's team don't, it's important to remember that she's trying to get Bourne all to herself at this point. Clearly that includes withholding certain information from her colleagues that she likely gleaned while debriefing Bourne's handler (Nicky Parsons) in the previous film.