Css webtools 3.1.2 is not loaded

I had the same. You need to add a static URI

in config.php i put it under application

return new \Phalcon\Config([
    'database' => [
        'adapter'     => 'Mysql',
        'host'        => 'localhost',
        'username'    => 'root',
        'password'    => '',
        'dbname'      => 'phalcon-time',
        //'charset'     => 'utf8_general_ci',
    ],
    'application' => [
        'appDir'            => APP_PATH . '/',
        'controllersDir'    => APP_PATH . '/controllers/',
        'modelsDir'         => APP_PATH . '/models/',
        'viewsDir'          => APP_PATH . '/views/',
        'pluginsDir'        => APP_PATH . '/plugins/',
        'formsDir'          => APP_PATH . '/forms/',
        'formsElementsDir'  => APP_PATH . '/forms/elements/',
        'vendorDir'         => APP_PATH . '/vendor/',
        'cacheDir'          => BASE_PATH . '/cache/',
        'baseUri'           => '/phalcon-time/', 
        'staticUri'         => '/phalcon-time/' // <------------------------------------------- here
    ],
    'settings' => [
        'development'    => TRUE,
    ]
]);

If that doesnt work add also the base URI

$di->setShared('url', function () {
    $config = $this->getConfig();

    $url = new UrlResolver();
    $url->setBaseUri($config->application->baseUri);

    return $url;
});

The credits go to this answer though. Thats what i found to solve it: https://forum.phalcon.io/discussion/15111/webtools-can-not-load-css-if-using-different-baseuri