What git is trying to say here is that the mode of the files have changed, the content of the file is still the same.
If this is common and the filemodes are not important for this project we can simply tell git to ignore this.
Either by telling git to do this as default or only for this project.
git config core.filemode false
Only for this project edit .git/config
[Core] filemode = false
And in case we do need to check in single filemode changes the following works
git update-index --chmod=(+|-)x path/to/file