Following a trained intelligence officer was never easy, the fact that she was a witch actually made it harder too. Tony had to be careful about tagging her with a locator spell. If he was too close when he shot it off, she would know and remove it, but too far and he may miss. There was also the possibility that she was wearing a protection charm against things like that. So while Tony had shot a locator charm at her, he had no guarantee it would stay.