I'm a contractor and I make my living doing remodels and repairs to homes. If I see something that I find suspect in a home, I bring it to the clients attention and explain it to them. If the client mentions something to me that they are concerned about, I address it right away. If they want something done a certain way, or fixed, then that's exactly what I'm going to do. Usually it's something small, like your floor, and I don't add anything to the bill. If it might be fairly involved, I tell them so and give them a price. Your contractor is working for you, he's being paid to do what you want him to do. Tell him what to do and if he doesn't want to do it, fire him and get somebody else.
When doing the repair, insist that they use glue and screws. Be sure they cut out as big an areas as possible. Ideally, you want a full sheet of plywood in the repair so that it covers several floor joists. The big no-no here is to have it span from two floor joists. That will sag and make noise for all eternity. Span as many joist as you can!!!!
Be sure of your width. A small difference in thickness will show with years of use. Insist that it is perfectly flat and that the seams are filled. There will always be gaps, it's the nature of cutting out the old stuff that it will never be truly straight or true. I use a straight edge for my lines, set the blade for 3/4 of an inch at try real hard to get a straight line. It's never happened, but I try. After the new wood is installed, I fill the gaps with Bondo. I like Bondo better then the other wood fillers. It's proven to be indestructable and impervious to bugs and weather. It sands quick and easy too!!!
Eddie