Some friends of mine built a high end house several years ago that I don't think it had as many problems as you are experiencing, the first major issue came when the contractor went to set the floor joists and found out that the concrete company poured the basement using the outside dimensions as the inside dimension so the joists were too short, so in turn that made the rafters too short too, the concrete company had an expensive oops there as they had to pay for all new floor joists and rafters. 

Once the floor joists were set and the sub floor was almost done my friends were there to check things out and the first thing he noticed was the stamo on the plywood that says " This side down" was facing up, he pointed that out to the contractor who said " I didn't see that" after laying almost 3000 square feet of plywood that was glued and screwed down, don't know that it really mattered that it was installed wrong but how can they crawl around on it all day and then say they didn't see the stamping ? There were many other issues but those are the ones I remember.