[BUG] 1.20 Missiles targeting my squad ships not selected enemy target

[YorrickVander]

So, trying to get around the issue of my owned ships dying due to my -20 to plutarch in storyline after capture mission, I was fending off a steady stream of fighters. When I launched sunstalker missiles, they homed straight in on my construction ship instead.

[YorrickVander]

Poking about with a game save editor I noticed that the construction ship wasn't included in owned ships section. Possible cause here?