If you hired an architect to draw up your house plants, they will typically stop by the construction sight to check to be sure the house is built according to plans and check that it is structurally sound. At least my architect did and good thing he did because the builders make a huge framing mistake. Turns out he read the plans wrong and I ended up with taller ceilings, a cathedral stairwell and a third floor loft (which was supposed to be a craw space attic!!). Rather than tear the second and third floor framing all down, the architect had the builder change some support beams and they swapped out the ceiling rafters for larger ones to bear the weight.
Now, if you do not have an architect, then perhaps you need to speak to your builder and get some of your questions answered. If you are not satisfied with the answers, which I would not be, especially with an already cracked foundation.....even efore bearing the weight of the house. Then I would summons the town engineer/building inspector to take a look-see.
Follow your instincts. Sure we are not all builders but we have the intelligence to look at something and see that it just is not right. Speak up. Seek answers before proceeding.