The solution is to accept that behaviour. You're on Windows so you should have autocrlf as true. It's there so line-endings in Git's internal records are consistent. The warnings are there so you can see if you're about to accidentally corrupt binary files during a commit.
Click Continue. If you want to prevent it happening on those files again, you need to unstage those files, then correct the line-endings and stage them again. Do so by changing the line-endings of the file to CRLF/Windows in your editor, or drop these command line tools into your system32 directory so you can do unix2dos some_file.java on such files at any command prompt.