Upgrade to from 15.0.7 to 16.0.1 sort of worked

So I ran the test on the apps before I started the upgrade and all apps were cleared as compatible. When the upgrade was complete, calendar, deck, and tasks were disabled with a warning about being incompatible. I went into apps, downloaded the three updates, and enabled them with additional warnings. Currently Deck and Tasks DO NOT HAVE the Official badge-- but do seem to still work.

Will there be an Official Upgrade for these? Why did the test pass those apps when they are not official?

In addition, I now have a warning about four missing indexes on the database, and occ returns that I do not have permission to execute the db:add-missing-indicies.

And even after clearing all cache- running the security scan issues a warning that I am not running on the latest version-- it sees 15.05.3 which I was running 15.0.7

Any guidance would be appreciated