From the system's POV maybe this is the right way to resolve the problem. Could masking the failure by obscuring this flight's waypoint problem have resulted in a potentially conflicting flight not being tracked among other flights? If so, maybe it's truly urgent enough to bring down the system and force the humans to resolve the discrepancy.
The systems outside of the scope of this one failed to preserve a uniqueness guarantee that was depended on by this system. Was that dependency correctly identified as one that was the job of System X and not System Y?