The owner holds two contracts including; with the designer (based on qualifications), and with the general contractor. For public entities, the owners are required to hire the General Contractor with the lowest, acceptable price.
The owner hires the Architect, the Architect completes the drawings and then the General Contractor bids the drawings.
If changes are necessary, the sooner they are initiated, the more cost effective the solution will be. A professional General Contractor will immediately notify the Architect and/or Owner of inconsistencies that may effect the quality of the finished product. It is far better (and cheaper) to build correctly the first time, rather than trying to correct a mistake later.