There is no fix that I know of. Once you tell the ship to do something it will execute the orders and then it will wait for a very long time before the AI takes it over again. Generally, it is a bad idea to do what you did during the game, to check on what the AI did.
Far better way to check what the AI did is to SAVE A REPLAY and watch it 
PS. What you did, however, is the best way to set up fights - for example, you want to test 30 assailants vs 20 illums with certain upgrades. You make a 1v1 game and switch seats repeatedly to make sure both players are on their way to having the fleet you want them to have and then you order both fleets to go where you want them to fight.
