That is not plywood. The dark spots are from the roofing paper being walked on, when the previous roof was applied and then removed.

When the underlayment is made dry by a proper roof repair, any mold must die.

Mold stains. If black mold gets on something, you'll have a black stain forever. It's even tough to get out with bleach.

Additionally, I see crumbling asphalt shingles. It could be asphalt dust. You should ask you roofer, not us. They were up there. I'd believe them if they saw no mold.

Typical looking reroof. Damp OB sheathing and asphalt ground in now. All good if they told you no mold, and were there even a little bit it would die quickly.

It's hard to tell what's going on in the pics, but I see batt insulation against sheathing, sloppy baffle installation, and a flex duct in one rafter space. It would indicate a cathedral ceiling.

It would be a good idea to investigate whether you have condensation. This is a risk in cold/hot climates (Zones >3) when you have batt insulation against roof sheathing and inadequate/improper venting, and not enough r value of insulation.