So this was City and not Tower or other building?
Did you get the battle screen?
Was there any unit defending the city?
Did you get "darkness" after closing the battlescreen (if you got battle screen)?
Does this always happen to you or only rarely?
Whats connection were you playing from when it happened? (bad connection?)
My fix in version 0.91 was for occupy of incomebuildings and towers, so I hope you shouldnt see this issue for them atleast. I was thinking occupy for city was working pretty well though, so I need to investigate this more...