The other day I was looking at my fingers on the fretboard during a technical exercise. After about 15 minutes, I had that nagging pain just like you describe under my right scapula. As soon as I stopped looking at the fretboard, the pain subsided. It wasn't just that I was turning my head to the left...I was leaning my head a bit forward (off axis) and turning it to the left. I often look at the fretboard and this doesn't happen, but obviously that day it wasn't ok. I realized that I haven't been to yoga practice for a month... so I went today.
It helps me keep a better awareness of the support I'm using for my actions. The fact that I didn't notice until I felt this discomfort is my signal that I need to reawaken my awareness.
As an inquiry, notice what you do with your shoulders when you look at the fretboard. Notice if you are leaning your head forward. This sort of position can cause all sorts of problems (back and neck pain) if you are not using enough core strength to support your torso and not supporting your head and shoulders properly with your muscles. Maybe it is a good time to take a deep breath and check in on your body's signals.
When the sun shines, bask.
Classical Guitar forever!