CR problems with thor generated files

[mraaroncruz]

I have been using the project catapult lately but I am getting some strange CR issues in my generated files (it uses Thor to generate them)
My app.css file looks like this
/*^M*= require_directory ./vendor^M*/
It is only adding these ^Ms after I write more text and line breaks to the file - the original file is ^M free - probably because it is all one line.

I am using vim and a Mac. When I yank all of the text, delete the file, create a new buffer, put the yanked text there and write the file - the CRs go away.

I remember having a similar problem maybe a year ago but I don't remember what caused it...
Thanks!