This is a known bug that has cropped up a load of times.
From tests from back when I was r6, I think what happens is that one of the players is gathering units to send into the city right next to the city. However as stacks are being combined one of them gets turnblocked. However because of the auto-move into city thing the stack then tries to go to the city after it has already fought in a battle. A stack cannot fight a battle in two places at once, and so the game goes into meltdown and just kills the stack because it shouldn't exist.
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