Has anyone ever had this happen? I have a villager who is a Master Scientist, Master Builder, and Master Farmer but is not an Esteemed Elder and does not have a totem. It has nothing to do with the Gong or anything else I can think of.

I assume that you have a lot of Esteemed Elders already. There are a lot of discussions about that hotly controversial subject. This is one of the most recent discussions, which will explain what you're seeing.

Thanks for the link. I assume that now there is no incentive to have the villagers master anything other than one skill.

If you're looking for the official Esteemed Elder title and the totem, then not really. Some people continue to train them and dress them in special clothing, though. It all depends on how you like to run your village.