You’ll have to prioritize your tickets so the MDX system, not the MB, deducts the correct entitlement:
~ go to Guest Relations or a Ticket Window to have the base ticket as the first priority.
Or, reassign the Hopper ticket away from that Guest’s Profile before park entry. Move it back to the Guest anytime that day. All FPs remain intact. This saves you from waiting in a line to have the ticket prioritized by a CM.