Editable registration date field in user profile

The user_registered field is not in wp_usermeta, but wp_user. You should be using wp_update_user:

add_action( 'show_user_profile', 'extra_user_profile_fields' );
add_action( 'edit_user_profile', 'extra_user_profile_fields' );

function extra_user_profile_fields( $user ) { ?>
<h3><?php _e("Información AbIbBEV", "blank"); ?></h3>

<table class="form-table">
<tr>
<th><label for="user_registered"><?php _e("Fecha de ingreso Empleado"); ?></label></th>
<td>
<input type="text" name="user_registered" id="user_registered" value="<?php echo esc_attr( get_the_author_meta( 'user_registered', $user->ID ) ); ?>" class="regular-text" /><br />
<span class="description"><?php _e("Fecha de ingreso del empleado."); ?></span>
</td>
</tr>
</table>
<?php }
add_action( 'personal_options_update', 'save_extra_user_profile_fields' );
add_action( 'edit_user_profile_update', 'save_extra_user_profile_fields' );
function save_extra_user_profile_fields( $user_id ) {
    if ( !current_user_can( 'edit_user', $user_id ) ) {
        return false;
    }

    wp_update_user(
        [
            'ID'              => $user_id,
            'user_registered' => $user->user_registered,
        ]
    );
}

You may need to adjust your other code to pull from the user’s data and not their meta.