Yeah it seems to happen when I'm standing still, I can send a video of where it happens too if that helps.
Is the steam version updated to the newest version? that's where I'm playing it and I'm still getting hurt by the pellets over there.
Very cool game! Although I think I might've found a bug where the shotgun sigil damages you while shooting it, its to the point that I cant get past the section where you have to shoot the walls down in the third level.