wp_insert_user function not adding password field to database

You don’t need to call 'pre_user_*' filters, that are called by WordPress inside wp_insert_user.

Also I suggest to use php filter_input or filter_input_array to sanitize form input.

Example code:

$args = array(
  'pwd1'       => FILTER_SANITIZE_STRING,
  'pwd2'       => FILTER_SANITIZE_STRING,
  'first_name' => FILTER_SANITIZE_STRING,
  'last_name'  => FILTER_SANITIZE_STRING,
  'username'   => FILTER_SANITIZE_STRING,
  'email'      => FILTER_SANITIZE_STRING
);
$form_data = filter_input_array( INPUT_POST, $args, TRUE );
$keys = array_keys($args);
$required = TRUE;
while ( ! empty( $keys ) && $required ) {
  $key = array_shift( $keys );
  if ( empty( $form_data[$key] ) ) $required = FALSE; 
}
if( ! $required ) {
  $err="Please don\"t leave the required fields.';
} else if( ! filter_var( $form_data['email'], FILTER_VALIDATE_EMAIL ) ) {
  $err="Invalid email address.";
} else if( $form_data['pwd1'] !== $form_data['pwd2'] ){
  $err="Password do not match.";  
} else {
  $user_data = array(
    'user_login' => $form_data['username'],
    'user_pass'  => $form_data['pwd1'],
    'user_email' => $form_data['email'],
    'role'       => 'subscriber'
  );
  $user_id = wp_insert_user( $user_data );
  if( is_wp_error( $user_id ) ) {
    $err="Error on user creation: " . $user_id->get_error_message();
  } else {
    do_action('user_register', $user_id);
    $success="You\"re successfully register';
  }
}

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