Was this part of roof and eaves done right?
The height of the fascia (the vertical face at the edge of the roof) depends on 3 parameters: Overhang depth, truss (rafter) heel height, and roof pitch (slope). 

If any of these things vary from one plane to another, at least one of the other parameters must be adjusted to accommodate. It's often simplest to have a slight variation in overhang depth. It's hard to say what impact that would have on your home from the photos provided. Judging by the fairly low slope you'd lose 6-12" of overhang to bring the fascias into alignment.

If you didn't work those things out with your contractor beforehand you may not have much recourse at this point. There is no violation of contract, and it's merely an aesthetic issue. If you're on good terms, discuss making a change and split the cost if the contractor doesn't agree that it was a mistake.