Capital Cities have shifted and replicated in other capital cities

All my capital cities in every civilization have been shifted and some of the capital buildings now exist twice or tripple in other capital cities, you have to vistit them and see for yourself. It is really bad, builidings in the water, buildings that overlay others and do strange graphic effects. I tried to delete the foreign civ buildings by repacking and then destroy and ended up having undestroyable buildings in my inventory. It is really bad, all my cities are messed up.