When I worked for Bella Vista Village (28,000 acres) Engineering Co., we found the most common defects in houses were improper plumbing. Drain lines were often level or ran uphill. On sloped lots, the next most common was septic laterals that were too steep, like 45 degree straight down hill....boy, bet that took all of 90 days to plug up.
One of the biggest disasters we had was on such a steep slope when the straw boss filled the concrete truck with water and dug a ditch to the footing, pouring the mix and run the mix that way. Of course, all the gravel was nearest the ditch and all the cement on the far side. Framed it up and came back to find the footing had broke into two and slide about a foot down hill. Framing looked like Leaning Tower of Pisa.
Similar was a huge room in one of the Company VP's new home. Engr.'s & architects spent days designing beams made of structural laminate beams and Big print on the blueprints to NOT deviate from the design. Carpenters took it upon themselves to frame by nailing Fir boards together then trim out the beams with Oak. Zip for strength. Framing collapsed overnight after the second floor was erected. Carpenters were drawing unemployment by dark. Supervisor was fired as well.
My pick of top 3 defects would be Leaky roof; bad plumbing; & inadequate ventilation of the roof.
In order: Proper flashing details. Properly, or even adequately, designed heating and cooling system. Compaction of the site prior to construction. Proper vapor barriers. Level and plumb (walls, doors hung, windows set).