A freind and I have tested this extensively. Playing a turn-based game over internet using 1.14f patch.
Whenever I kill the last unit in an enemy city with a marine from a transport, an out-of-synch error occurs as soon as another unit (be it marine or land unit) enters that city. The marine who killed the last enemy unit does not take the city, just leaves it empty for the next unit.
restart the game using the special out-of synch save, then you see that I have taken the city. But only the second unit is there, the original marine is gone (and he's not still on the transport either).
This bug has to be fixed as it basically takes marine (which I luv) out of the game. One way to really piss off your multiplayer opponent is to take a city, and then have to restart the game once you have done so!