First of all who is the housebuilder.
Secondly, I assume you are talking about front and back external doors as internal doors don't have a "bottom sill" other than a carpet gripper.
Quiet how they could accuse you of changing hinges is beyond be.
It is very simple to adjust hinges to raise the door or at the worst, take the door off and plane the bottom (if it is not uPVC)
The fact it was picked up by your snagger also means it should have and could have been sorted out before you moved in.
I have no idea why they are making such a fuss and resistance against something so simple to sort out.