Hi,
HikaShop has no tracking ID for orders by default.
So I suppose that you must have added some way, probably a custom order field.
Note that we've added extra display options for custom fields with HikaShop 3. So make sure that the display settings are correct for your custom fields and save them once.
Also, if you still have the problem after that, check the emails in the menu System>Emails. You might have overridden them and the preload of the emails have some code modification in order to support the new options of custom fields. So you might have to delete the preload customizations and reapply your changes to the new version of the preload if any.