The issue you described has nothing to do with PHP or jQuery. I have isolated the issue you have described down to:
<form action="http://www.google.com" method="POST" enctype="multipart/form-data">
<p>Select a file, for example z.txt, then before clicking submit,
rename the file locally so the file picked is invalid, such as zz.txt,
then submit to get an error in chrome.</p>
<input type="file" name="myFile">
<input type="submit" />
</form>
Yes, it doesn't even matter where the form sends to. Chrome will error if the file doesn't exist before it tries to send. Firefox, however, will submit the form as usual. This is an issue with chrome. You can, however, adjust chrome to hide network messages:
Suppress "Failed to load resource: net::ERR_FILE_NOT_FOUND" in Chrome Packaged App