They should really just have an "all-or-nothing" option for waitlisted upgrades. If not all of your upgrades can be confirmed immediately when you request them, you can opt to stay on the waitlist until there's availability for all segments.

Not ideal certainly, as you'd probably miss out on some upgrades where the long sement clears before the shorter one, but it's better than wasting a CR-1 on a 200-mile flight.