First, if you have a contract with someone, and a question/suspicion arises about the work specified in that contract, you should just ask the person you are contracting with, rather than go online looking for guesses. We have no idea what happened in your scenario unless you tell us.
Second, what do you mean by "his crews"? I assume you spoke with and made a deal with one person... that's pretty normal. However, did you expect or specify in your contract that only this one person was allowed to build/install your roof? That's highly impractical and would no doubt be far more expensive, because it would be far more dangerous and take far more time to complete (read: hourly rates + hazard pay). It sounds like you hired a "company" so I don't see any issue with "the company crew" doing the work?
Third, this is part of the benefit of using a contractor; they have connections with other contractors they can "sub" work out to based on their expertise. If a general contractor has a good business and customer service acumen, it makes perfect sense (and is more efficient) to sub out the parts of building construction to smaller crews who may be really good at doing the building, but not so good at getting work for themselves from homeowners/people "outside" the construction industry. Painters want to paint, framers want to frame, and roofers want to roof. They don't want to haggle with first-time homeowners Bill and Pam about price and materials and deadlines... let somebody else do that.