As of the January 2023 release, how extraction zone coordinates are calculated has changed. During the upgrade of your instance, the upgrade process will run a command that recalculates these coordinates.
However, this process may not work accurately in all cases. If this happens, you will have to reload the template file, so that the pages and zones are recalculated again.
For new templates, we recommend using the convenience of the new functionality that allows you to create the template from a document.