having worked at the project manager on a large scale residential high-rise and dealing with change orders, RFIs, and the sort...you get to know that every single job has problems. Architects forget or overlook something that an engineer now must have, redesign. Mechanical needs to be where electrical is, redesign. etc. etc.
good supers, i mean the really good ones...can spot issues on blueprints the day they are dropped off and then can call a site meeting weeks or months in advance of that work being done to rectify it.
however, many onsite issues happen such as severe sloping of cured concrete or even bowing between columns. These all have tolerances and they can often be fixed after the fact.
Basically the head project manager and site super are responsible for these along with the head consultants. Goes to show you how important interfacing is and how site meetings can resolve problems before they become "major issues"
"The destructive effects of automobiles are much less a cause than a symptom of our incompetence at city building" - Jane Jacobs 1961ish
Wake me up when I can see skyscrapers