I've got the same issue; you can see videos here: https://www.youtube.com/watch?v=ra6zLuTul9Y and here: https://www.youtube.com/watch?v=mpHECmmPhSY
After about 30 minutes of usage when writing in OneNote on my Surface Go with the Surface Pro 4 Pen (the one with the clip and grey eraser), the Surface freezes and then every time I touch the pen to the surface to write, the entire screen flickers black. It also happens in other apps like Sticky Notes. The issue resolves itself upon restarting, but starts flickering again another 30 minutes of writing later.
This basically means the device is useless for the main purpose I bought it for, to take notes in class, as I don't really have time to reboot every half an hour in a 2-hour lecture.