Holes in shingles from scaffold anchor points. How will I know how bad the decking was affected? Ask for $ from siding company?

New roof 4 months ago, new siding 3 months ago.

Noticed a large yellow spot near my vent on my 2 floor. After raining, the water started coming through the vent.

I called out my roofing company today. They brought me up to the 2nd floor and showed me holes in 4 different locations. They then asked if the spiders scaffolds. I said yes. They go that’s what we thought, then showed me all of the holes.

They said because they did not caulk the holes, water began seeping in.

There are 3 (I initially saw 2) deck boards that are now darker than the rest. During the rain, they are wet.

What’s a reasonable ask? That the siding company pay for new shingles in those locations? What about the decking? Do I need to worry about it getting wet for 4 months?

What about the insulation (which is wet)? Finally, what about the drywall?

Is it likely my siding company will pay for all of this? If not, do I need to file a claim so that my insurance company will fight their company?

Thanks.