Ran into that situation as well. Even with a clean environment. You should start with a clean environment and try to apply the patch. Revert it when done.

When applying a patch fails you need to create or delete files manually depending on why it fails.

Patches only apply changes to files. They don't correct your environment, you need to do that yourself. What you need to do depends on the situation. Not all patches can be tested this way.

I'm tracking an issue with when a patch includes binary files, those aren't getting applied correctly. But changes to text files (PHP, CSS, JS) should be fine as long as file permissions in your environment are good. Just note I would HIGHLY encourage using the patch tester against a nightly build (http://developer.joomla.org/cms-packages/) or installing the current GitHub master (https://github.com/joomla/joomla-cms/archive/master.zip). The patch tester doesn't actually patch files as a client side patch tool would (either using git on command line or through your IDE), it's actually completely replacing files and making a backup of the file it replaces so when you click the revert button, you're restored to the correct state. Something I've not looked at is what happens if you're testing two patches touching the same file, and I can see that causing issues, I'd just need to think through how to work that out.

It won't allow you to apply the second patch when one of the files is already patched. That is based on the file already existing in the backup folder.

Which means you have to revert the first patch.

Based on what's here closing as expected behavior plus a lot of the underlying engine has been rewritten in the last couple of years.