New roof, but moldy plywood in 5 months?

This past summer I had two trex decks and a post and beam roof structure built and installed. the roof has 4 skylights, is shingled and the underside of the roof isn’t finished yet. In December I noticed water drips on the deck and water stain on the plywood in the roof peak closest to the house. A couple weeks ago I noticed the plywood on the underside of the roof spotting black. At first it was just one section but it is now spreading. Our contractor says plywood does do this and this is not a roofing or shingle issue, but clearly a product issue. He suggested we reach out to the mill regarding the plywood?? I should mention, it was confirmed that the flashing kits were installed incorrectly. He has ordered new ones, but could there be moisture in the roof and that be the cause?

That plywood Underside needs to be stained or coated.

Pictures of the skylight install? To screw up 4 skylights is pretty rough.

Yeah that’s definitely wrong. Columbia skylights?

Yes, Columbia skylights.

I originally planned to finish the underside with 1x4 t&g, but since the project went later into September I decided to wait until this spring to finish it. Is your suggestion only because of the mold? Or is it something I should have had done before winter? The contractor never brought up coating it

Notice how the mold starts one foot away from the ridge which just happens to be where the roof above it drains into it.
You have discovered a problem with the roofing
And your roofer is denying it.
Dont finish the ceiling untill you know that the problem has been addressed.
I’d spray it with some bleach in the mean time.