I just had a new roof installed and I noticed this oddity when the crew was doing the work. It looks like the plywood in the circled area is bowed and I can see obvious space between that and adjacent pieces of plywood. This piece of plywood was not replaced. I talked to the contractor and he said he is not concerned about this. Should I be concerned? He has offered to re-do this part of the roof, but said it will be "intrusive" and does not recommend it. Any suggestions?
Yes, you need to concerned if you think that the issue is not resolved. You can talk to other roofing contractors about the problem for better advice.
IF the sheet is only spanning two rafters fix it the right way with a sheet of plywood that spans at least three rafters. Otherwise you could simply put a couple 2x4 or 2x6 under it for a little extra support. Chances are that there may have been some moisture that got in from the skylight causing a little warpage.
the plywood is supposed to lay flat with a 1/8" space between the sheets.