If the plans aren't to code, question it! A lot of the problems between engineers and contractors stem from miscommunications; no sense making a mistake on paper more expensive with malicious compliance. If it was a mistake, then it's a mistake and it's a good thing you caught it. If it was a deliberate nonconformance, then you'd want to know the background and/or get it in writing so you can cover your ass and put the onus on the engineer.
The appendecies of the IRC has a paragraph stating that the codes are not meant to stifle innovation and that exceptions are allowed. (I mention this because my state, like others, didn't adobt the NEC directly, but only through the IBC, in which case, as I understand it, the IBC would have override the NEC.) If the non-conformance was done for a reason and has sound engineering data and a stamp to back it up and was approved by the inspections dept, then you'd at least feel better about doing it like the plans, right?
