Here is the bug, you create a scenario (see my ww2 scenario also to see the bug start as the commonwealth) and give the Pyrs to a player, some of the cities won't have the granary!!!

Link to the scenario? Game save?

@ Chieftess, just see my signature, there's the link to the scenario with game saves.,,,

Are you sure it isn't just that some of the cities aren't on the same continent?

no, the city I noticed it on is just next to the one that has the Pyrs...