WP default file upload hook not working if used in a plugin

maybe validate_user_storage_space is firing too early or its too late. try wrapping this function inside another function then hook second function with one of below action hook

init or after_setup_theme or plugins_loaded

like below.

add_action( 'init', 'validate_user_init' ); //after_setup_theme plugins_loaded
function validate_user_init(){
  add_filter('wp_handle_upload_prefilter', 'validate_user_storage_space', 1);
  add_filter('wp_handle_sideload_prefilter', 'validate_user_storage_space', 1);
}

function validate_user_storage_space( $file ) {
 //your stuff
}