Thanks for the response. I’m still doing a bunch of testing on my end and have a back and forth going with the Jetpack guys. The latest thing I’m finding is that it’s not necessarily your plugin, but not allowing site stats to activate upon connection. If I remove your plugin and just use code to whitelist modules AND allow site stats to auto-activate, everything is fine. If I turn off auto-activation for site stats, and the user has to manually click on “Activate Site Stats” – that’s when the error comes in. This occurs on any multisite installation I’ve tested on, even with no other plugins active. Haven’t nailed down anything definitively yet.

Yes – it’s the default jetpack hook. I’m keeping ‘protect’ as auto active but have been toying around with site stats being turned off/on from auto activation.

function custom_auto_activate_modules() {
    return array( 'protect' );
}
add_filter( 'jetpack_get_default_modules', 'custom_auto_activate_modules' );

Hey – sorry for the miscommunication here. Nothing to do with the ‘protect’ module – just the site stats. What I’ve found is that if I have the plugin set to not auto-activate modules, then the user has to manually activate site stats. If the user has to do that, then they get the console error mentioned above. If I allow site stats to be auto activated, then everything is fine.

Yes – I’ve tested on 3 different multisite installs and getting the same functionality on each (one with subdomains, one subdirectories, one with hyperDB as well and domain mapping). I’ve tried on a fresh multisite install as well, wordpress 4.7.3 and 4.6.3 and getting the same deal every time. Here is a quick screencast of exactly what I’m seeing: https://screencast.com/t/QCjKlcCcFfZM