When using hook_FORM_ID_alter(), with FORM_ID = menu_link_form or FORM_ID = menu_form (at least, maybe others as well), the form_alter hook is called twice (I'm wondering if it's because in these cases, FORM_ID = BASE_FORM_ID).
As a side note, when debugging the form, the class attribute contains two 'menu-form' (or 'menu_link_form') classes, and the '#theme' array contains twice the same key either.