The dumb counterfactual assumption but "logical" reason is they already have a working facial recognition profile of everyone without a mask but they need more masked training data to work around it and can't simply digitally add a mask to their old training set.

Contradicted by what we know about current facial recognition technology but in a "make sure that the bullets are sterile, we don't want any wounded prisoners to die of an infection before we get any intelligence" sort of way.