If you want to disallow the indexing of the Hatchbox domains for your apps you can do either of the following:
Set up your robots.txt for that domain (your app should respond to that route instead of using a static file)
Customize your app's Caddy routes to include %{hatchboxapp_robots} which will set up a robots.txt for that domain to deny all. You can find that Caddy config under the app's Edit page.
Set the canonical meta tag on all pages with the correct domain to ensure that pages indexed are corrected.