To simplify the steps between scanning the QR code to open the filter, and then using the filter, we opted to use the QR code as the initializing image, which meant we needed to use the picture of the QR code for the on-screen instructions. But this seems to be causing our filter to be rejected for having a QR code present.
The policy stating there can be no QR codes is a subsection for preventing links to outside sites, so we thought it should be fine since this QR code points to the Instagram link for our filter and not to an external site.
Apparently, the context of the subsection is not limited to the context of its parent section. We solved this by using a separate image to trigger the effect, but the cost is that a separate image was needed to trigger the effect in addition to the QR code to download it.