By default when we create a page within episerver, two of the categories are ticked automatically.
Is there any control over this to stop it from happening?
Has to be some code that does this. See if you can find anything subscribed to the Saving and Publishing events of the DataFactory class.
You could also check this blog post, which can detect what code is attached to the Page Events
That is by design, categories inherit the value from the parent page when creating a new page.