Most definitely. They still can be filled with an appropriate colored wax pencil.

What circus did you hire those clowns from?

You should be giving a written list of items needing correction to your contractor. And keep a copy for yourself. Hopefully, you're inspecting everything at least weekly.

I've been debating whether to do this on the cherry trim I've installed myself. Most fill I've ever seen or done is much more obvious than the finish nail holes, so I'm not at all sure that filling the holes would be an improvement. A big problem is that even if you match the color now the wood will change over time and the color match won't hold up. There's also a big board-to-board variation, so color and grain matching would have to be done hole by hole, which would, I think, take forever. I'm currently thinking I'm going to be happier without fill. I'm not sure there's such an obvious "right" answer for stained trim--for paint I'd definitely fill.