Buildings not exactly matching the architect's original design is so common that there's a term, "as-builts", for the set of drawings the prime contractor prepares and delivers along with the building, showing what was actually built (hence the name) and, by comparison with the originals, what was changed in the course of the build.

I'm not the right kind of engineer to hazard a guess as to whether this is an unusually high variance for this scale of project. We also don't know what "failed to conform" means - the language is as vague as, given the ubiquity of changes at build time, intentionally pejorative. There's really not enough here to judge either the architect or the contractor; it could be a brilliant design badly implemented, or it could be a terrible design the contractor did their best to make work, and no one here or in the NYT article, including its writer, has enough information to say which.