1) Your contractor doesn't give you a detailed quote. This is often because he's not pulling permits, so the quote wouldn't include a line for the building permit costs, which would be (or should be) an instant red flag for the homeowner.
2) No plans or drawings are submitted. Permits require drawings or plans. If the contractor doesn't have any, guess what? He also most likely does not have the permits.
3) He does not offer you a copy of the lien waiver once the job is completed. This is an important one, as it ensures that you are not held responsible for the material costs from the companies the contractor has not yet paid.