It is attempting to rewrite CRs and LFs into a consistent format. That is, it doesn't see your binary file as binary. To force git to do this properly put the following line in .gitattributes:
*.bin -crlf -diff -merge
From this page that means:
all files with a [.bin] extension will
not have carriage return/line feed
translations done, won't be diffed and
merges will result in conflicts
leaving the original file untouched.
