On the True Nature of Passports vs. Citizenship R (Bancoult) v Secretary of State for Foreign and Commonwealth Affairs (No 2) [2008] UKHL 61

On the True Nature of Passports vs. Citizenship

This case heavily debated the constitutional right of citizens not to be exiled or removed from their territory.

The Principle: The courts recognized that the right of a citizen to reside in and enter their own country is a fundamental common-law right that cannot be casually stripped away by executive or administrative maneuvers.
Application to your scenario: Because citizenship is an inherent constitutional status and a passport is merely peripheral evidence of it, a citizen's physical expulsion by a non-authorized actor cannot alter that inherent right. The state cannot use the absence of the "proper document" at the border to justify why a citizen was sent away, because their right to be there is anchored in their status, not their booklet.

If this case went before a high court today, judges using Anisminic and Lazarus Estates would rule that:

The traveler was never legally deported.
The traveler does not have to file "applications" to fix this, because a victim cannot be forced to trigger an administrative remedy for a purely criminal event.
The state must bear 100% of the logistical and financial burden to undo the nullified action and return the citizen to their home.