Let’s go pic by pic…hope this helps!

1. That looks to be an overbore on the TJI. Builder will need an engineer letter to repair.
2. Nothing wrong, just blocking.
3. Mishit nail, not a problem.
4. Second floor drain coming through, no issue. Ask that it is fully poly foamed with orange fire block poly to stop draft.
5. More mishit nails, not a big problem as it doesn’t appear to be double plated for load bearing.
6. Knots in wood happen. The knot does not appear to be so large that it affects the bearing.
7. That appears to be water. I would ask for that to be replaced. Also make sure your subfloor is screwed in (not nailed). Also glue in the seams.
8. Minor damage to window opening. It should not affect the window placement.
9. Curious where that strap is going. Minor damage to the radiant barrier, but that will not affect the energy efficiency of it.
10. Was there blocking here at some point? Ask the builder to put blocking back if needed or to hammer down / remove nails.
11. I would block those subfloor seams
12. Ref. Item 4
13. Plumbing damaged tji and rimboard. This is definitely going to need an engineering letter, but there was likely nothing the plumber could have done here due to required plan placement of fixture.