Was discussing this with some other officials - I think they correctly identified the issue, in that they said (paraphrasing) that it's real easy to get into "groupthink" and just assume that what you're being told, or what someone says, is accurate and correct.
That's a difficult bubble to break out of. That said, I have seen an RO stop the game to discuss an on-field penalty enforcement with the R - he believed they were enforcing from the wrong spot, and when the R came over, he he realized that the hold occurred during the kick, therefore enforced from the end of the kick, not the end of the run. Was a brainfart moment, but it happens, but at least he was willing to say "this doesn't seem right" and he spoke up.