The issue is that git is replacing the line endings of the Mac libs from \n to \r\n. Clicking repair when this popup appears will switch them back to \n, but it looks like git is still clobbering the line endings every time you pull.
Deleting them if you don’t need them is one option, otherwise if you add
*.bundle text eol=lf
to your .gitattributes file then the line endings of any .bundle files will remain as \n (line feeds).