I have looked into the game. I could not identify any abnormality, though.
In the respective battle casualties have been chosen (technically) correctly.
Because you report that casualties might have been selected automatically and in a way you did not intend, I suspect that the following might have occurred:
As you have played a game “Human” vs. “Human” (not involving an AI) you will always be prompted for casualty selection in case there is a choice between different units. Indeed, TripleA follows its own logic when suggesting how to assign hits. For example it will always damage capital ships before taking out units - and when taking out units it will take out units with a lower defense value rather than with a higher defense value, or prefer to take out cheaper over more expensive units - I don’t know the exact logic, however. Many times this logic appears to be adequate, but there are situations where you would prefer other selections, for sure.
Anyway it looks like you might have accepted those suggestions in the heat of the battle by confirming them. At least that is what happens to me from time to time, when I do some testing “Human” vs. “Human”.
So for now I would really recommend you to “speed down” the game by following the above tips.
Please report back, in case you experience similar situations.
Enjoy gaming :-)