Well I am pretty sure it was my modification that caused this. I looked at the computer empires designs from this game and the game before I made the modification. The computer was for some reason replacing the supply storage units on their design with an extra engine instead. Maybe because my level 2 engine has 550 supplies and a level 1 supply storage unit has only 500
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Well here it is if you want a more challenging game this mod will give your opponents a speed advantage in battle with some of their ships. The ones that are already propulsion experts move very fast now. It only seems to happen in light cruisers and above.