According to what the devs explained quite a while ago, that is usually caused by multiple AI fleets arriving at the same planet simultaneously and attempt to autoresolve the battle, which the game is not prepared for.
Launching a massive aggression against one of the factions before they send the fleet may be a solution by interrupting their strategy and making their fleet go other place, however it seems that for your condition that is not quite optional...
Just a reminder, have multiple save files can reduce the loss cost by such bugs.

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According to what the devs explained quite a while ago, that is usually caused by multiple AI fleets arriving at the same planet simultaneously and attempt to autoresolve the battle, which the game is not prepared for.
Launching a massive aggression against one of the factions before they send the fleet may be a solution by interrupting their strategy and making their fleet go other place, however it seems that for your condition that is not quite optional...
Just a reminder, have multiple save files can reduce the loss cost by such bugs.

Thanks for your suggestions! Saving a lot really helps.