For example: https://github.com/rob3n/yard-frontend/pull/4/files
https://github.com/rob3n/yard-frontend/blob/770ad32d0b60f42aff3c7e61edb5fbfdaecb5bc1/public/index.html

But file have spaces

I'm seeing this too. I think it's only for diffs that are loaded later.
Located issue: it's removeDiffSigns
Uhh the whitespace is collapsing once it's no longer prefixed by a - or +. The cause seems to be pre-wrap but I'm not sure if we should disable that. This looks like a headache.

Hi, I installed today refined-github the first time. I also experienced a related bug with whitespacing. This bug here is not the same, but may get fixed in the same time.
My commit adds a single line without any preceeding whitespace, but it get's displayed with a small extra indentation (which is confusing).
Correct: (plain github)

Wrong: (refined github enabled)

The Raw commit is here: dunst-project/dunst@717c747a8caf0f823da0e4e45bbb632ef46c68ee
Weird. I don't see the issue in the OP at all (perhaps because I'm using Firefox).
I can recreate https://github.com/sindresorhus/refined-github/issues/590#issuecomment-313931801 however; moving it to a separate issue.