I think i know the reason why i'm experiencing this. Since you suggest that when you phase the ship time would be slow. I put my commander in a non phase ship and the battle ran normally, but when i put my commander in a phase ship time would slow when that ship phase.
So it's not a bug but just game design, if i'm controlling the ship slowing down time is awesome but when i'm micro managing the whole battle that could be a little annoying. If you could disable the function when commander ship is in auto pilot in the next patch that would be great. If not, you could put it in the tips so everyone can be aware of that.
Anw, thanks for the help I really appreciate it. Beside, hope that one day you can make this game multiplayer and put it on steam
. I would love to do battle with my friend.