I just ran sudo pacman-mirrors -ic Germany and selected the three top listed mirrors.

Feedback:

.: INFO User generated mirror list
--------------------------
.: INFO Custom mirror file saved: /var/lib/pacman-mirrors/custom-mirrors.json
.: INFO Writing mirror list
   Germany         : http://mirror.philpot.de/manjaro/unstable/$repo/$arch
   Germany         : http://mirror.philpot.de/manjaro/unstable/$repo/$archunstable/$repo/$arch
.: INFO Mirror list generated and saved to: /etc/pacman.d/mirrorlist

As you can see the http philpot mirror is listed twice, once with a link containing /$archunstable/, which doesn't seem right. The https link is missing, so is the third mirror. This is also what /etc/pacman.d/mirrorlist actually contains. Content of /var/lib/pacman-mirrors/custom-mirrors.json:

[
    {
        "country": "Germany",
        "protocols": [
            "https",
            "http"
        ],
        "url": "http://mirror.philpot.de/manjaro/"
    },
    {
        "country": "Germany",
        "protocols": [
            "https",
            "http"
        ],
        "url": "http://mirror.philpot.de/manjaro/"
    },
    {
        "country": "Germany",
        "protocols": [
            "https"
        ],
        "url": "https://repo.rhindon.net/manjaro/"
    }
]

So, the third mirror is listed here, but again philpot http twice, and not the https version. Another time I had selected two mirrors, ragenet and netzspielplatz and only netzspielplatz got listed. Somehow I cannot reproduce this now, but something seems to not work properly here ...