hook form submit being called twice
hook_form_alter() will fire once for every time there is a form on the current page. 

You can try the hook hook_form_FORM_ID_alter(). This will only run once when the form with the specific ID pops up. 

Unfortunately I had this issue happen before, the hook_form_alter() ran multiple times. I stopped the code from running multiple times by encapsulating the code inside an IF statement inside the hook_form_alter() example: if($form_id == my_id). So the hook ran multiple times but the code only ran once.