I have weird problem when some files, especially shader files are marked as modified in git status even though they are unchanged. I’m using git 188.8.131.52 on Mac. The problem is consistent across different version of Unity.
I’ve experienced similar before with shaders - typically, this happens when I’m changing the shader via script, usually because I’m changing the offset to create a movement effect.
If that’s the case, you’ll continue to have this effect unless you switch to modifying the renderer.material (instead of the renderer.material, or just the material from your project view).