Licensed Contractors' civil responsibility and integrety

[John Ma]

Hey guys, I hope someone who may have been around the block may be able to steer me in the right direction.  This is my first time working with a sub-par contractor.

I had a roof replaced recently (shingles and boards). I am not completely satisfied with the outcome, however it is acceptable for its roofing functions.  To have it done to what I want, it would basically need a re-do down to the joists.  During the work, i was lied to about what the joists looked like, which I later found out and had repaired afterwards from the inside.

With that said, I have not paid the bill in full yet and want to re-negotiate the contract based on the outcome.

To have some leverage on negotiation, I want to know whether it is a Licensed Contractor's civil duty to point out things that not to code and not continuing with the work until that is fixed.  I assume this is something that would jeopardize his or her license?  

What is a contractor putting at stake when he/she does not get permits prior to performing work?   I suspect this was done also.