OK, so I ended up contacting Microsoft support for this since, as of this date, there is no information on this error message.
To put it briefly, Microsoft has made some recent changes with regards to permissions. In the past, if your app required any of the openid, profile or offline_access, you could just place them in your app as scopes, they weren't available on https://apps.dev.microsoft.com. An admin would've given consent and your app would function properly.
What you should now do is mirror your app's scopes with the permissions you have on https://apps.dev.microsoft.com or else you'll keep on getting that error message so make sure you have the same thing on both sides now, especially if you're used to the old behavior.
Those three scopes/permissions (openid, profile and offline_access) can now be selected for your app on the dev portal.
