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think that's another bug. i had that too. sometimes when the enemy builds a building in their capital, the city rotator widget at the top right switches over to showing their cities, meaning you can take a look at what they've built but you can't build anything in your own capital. either move a stack into your capital which will bring up the capital in unit view mode, and from there you can navigate to the right construct building screen, or save and reload, which seems to reset the city rotator widget at the top right to your own cities again (until the enemy builds another building)
This is a bug. A workaround is to save your game and reload it and then enter the citiy if this city switching bug happens (cumbersome). The easier way is to get the patch (provided on kalypso media´s website/forum or via your digital download provider) which removes this bug.