Not sure if this is something to be concerned about, but in my experience, you want the fascia board installed before the shingles go on. The reason is that you want the flashing to go over the edge of the fascia boards. In your picture, the paper is on already, but not the fascia boards, which means it's going to be hard to tie the flashing in with the paper.
What are you using for the fascia and soffit? I'm a big fan of Hardie because it doesn't rot. Cedar and treated wood will rot in time. There are other brands, but PVC vinyl is the only other one that I know of that wont rot, it's just a lot more money then Hardie.
I'm curious how they will trim out your soffit at the gable ends of your garage. In the pic, it looks unfinished, which means they are going to get to it, or they are doing something weird.
Eddie