Why hook_form_alter implementation is being called twice?
I ran into the same problem today, a hook_form_alter() override in a custom module was being called twice on every form.

My custom module's name was "project_name" and my theme was also called "project_name" (folder/machine names). I uninstalled my custom module and renamed it to "project_name_different" and re-installed it. After that change, hook_form_alter() only gets called once.

Don't know the super technical explanation for this answer, but generally Drupal doesn't like duplicate names across modules and themes, so make sure machine names are unique across all modules and themes living within your site.