First off.... I'd look into the actual details of this 'warranty'....
Especially who is backing the warranty and where they are likely to be in 10 years. Also, "limited warranty" is about as scary as everything else. If you are going to invest a good deal of money and you are determined not to run off screaming, which is what I would do, then I would consider having an attorney take a peak at that warranty too - especially if there is ambiguous langauge involved.
Bottom line to me is simple this - for industries like this, I typically think of pride of workmanship as the best barometer to trust people's work. In this case, I think the fact that these sloppy things were left undone for inspectors to see for anyone to see speaks volume.
FWIW: The bricks are not under the foundation, they are on top of the foundation (typically). I wonder could there have been a change in plan for the exterior, or if this is an indicator of some other construction fault.