Install and update the version you want to run. If you want to run Core, install Core and update Core. If you want to run Knots, install Knots and update Knots.
The confusion is due to the fact that on StartOS both Core and Knots are “bitcoin” and so they appear to both be installed and updates for one may appear to be for the other. In your case, you had Core installed that had a version slightly lower than the latest version of Knots, which means StartOS believed there was an update for the one, the other or both.
This is the tradeoff currently to allow for Knots to exist on StartOS currently (which a lot of people want for both practical and political reasons), and is something that will be fixed in the future.
If you clicked to upgrade from Core to Knots, by clicking on Knots and then clicking upgrade, then you have made an active choice you switch to Knots. If this was somehow accidental, you’d go to the marketplace, go to Bitcoin and choose to reinstall Bitcoin. (Go to System and click on the heading Manage 5 times to enable that reinstall button if you don’t see it)