I’ve had the ship thing happen and what I think is happening is ships are stacked and it doesn’t say they are stacked and you may have engaged a different ship. I’ve destroyed 3 ships on top of each other and I was like what the heck at first but I am now pretty sure that was what was happening.

"I stopped playing minecraft prison serves to try my first Civilization, and I'm a little amazed at the quality and difficulty of the game.
Everything is very deep and worked  a little slow, which I was told is a part of the Civilization franchise. So, I tried not to pay attention and not to give so much importance to it.
As you mentioned, I was surprised that I've started to loose battles. I ended up suffering a considerable loss.
I don't know if I missed any information, but that's what I felt"

Combat seems to get bugged the longer you play a game. If you look at the combat log, it uses the wrong ships, Usually quitting and restarting will help for a while.