I know it is vague, sorry
I can tell you it is actually not from Git, as it does this even when git is not active. It may be if you click or change something while it's autosaving, but since the program is mostly frozen, it doesn't always work.
I will experiment with it some more and if I find steps to reproduce it, I'll let you know. I just posted it here for reference and to see if anyone else experienced it.
Thanks for reading though!