On rare occasions, the Utility Wand spawns one or more ships too many when using 'Fill board with random ships' in Shift Mode (pulling from all ships instead of the ones in your inventory) without adjusting the HP of the fleet. The game still ends once the fleet HP is reduced to 0, causing the game to end before all ships are destroyed.
I have not been able to find a way to consistently reproduce this, making it very hard to identify the actual underlying issue..
If anyone finds a way to reproduce this, please post an issue or comment on this one to let me know how to reproduce it. Should you ever encounter this issue, it is recommended to not save/use the generated configuration and make a new one instead, since you will most likely run into issues if you decide to use the configuration.