It amazes me that people can do such terrible work with above ground based piers like that in the warmer climates.. when I build where i live for home owners I need to be 5 1/2ft in the ground with sono tubes and the top level or id be laughed off the job by the homeowners I do work for. Sadly Some companies feel efficiency is better than quality.. I would definitely ask them to redo the poor work areas now and coming from a contractor if they aren't willing to correct it at the rough framing part of the build the rest of your project will be a battle and you'll find yourself micro managing them which will only increase the tension on both sides and you won't be happy in the end and that's not where you should be.