I have seen this bug happening during Age of Abondance on PC. The empty banners stack on the same tile, while some AI cities and Encampment don't display their city banner and Encampment's banner at all.
Perhaps it is related to the Standard ruleset (never had this before). Perhaps it is related to some mods, or due to mods being deactivated after a reload.
I could also see M'Banza icons too like we could se on the "Empire" lens (but without the "Empire" lens). I had a bug where I need to restart my computer because I couldn't see the tile yields (but I blame a mod, not sure if related). So so perhaps it is linked to districts in generals, City-Centers and Encampment being more visible since they have a banner related to them?
I will conduct more tests to see if there is a way to make it happens consistently.