Scientology is revolting, but Cruise has every right to demand precautions on set. Audio here: https://www.youtube.com/watch?v=tHteO55JzD4

Sounds to me like the rules were clear and some of the crew broke them anyway. So fuck them, because no one wants some asshole breathing in their face for a full shoot. They spread any infectious disease and it affects the whole production. Is it annoying? Is it possible that masks don't do a damn thing? Yes to both, and no, it doesn't matter. Change the man's mind by providing evidence that conflicts with his belief, or fall in line. Totally different expectations at a place of employment, as opposed to a private residence or some public area.