If you create a release using the Bundle Builder and the track is already assigned to a Contract In, the system will then automatically add that track to the relevant Contract In to save you time.
You can prevent a track from being automatically added to the Contract In by going to Settings > Royalty Settings > Change Auto Add Bundled Tracks to No
You can also set this on an individual Contract In level, by setting the Auto Add Bundled Tracks option to No on the relevant Contract In.
NOTE - Clicking Update All Contracts will update the Contracts In going forward, but will not remove any already added.