Prevent File Upload during an ajax call
Drupal submits the entire form at every ajax call, I think you'd have to use hooks before submit, before send or similar to prevent it. Heres something to get you started. Or simply put the file field last or at least after the ajax form elements.

Disable all form elements when doing AJAX

Ideally drupal should allow you to specify what you want to submit. please share your solution if you figure it out.