Help with TC plug please (EV)

I'm currently building a total conversion plug for EV, and then soon after I will convert It for EVO. However I have stumbled across a few bugs, I can't fix... help please.

A Major Problem is:

I have two major government factions that are conflicting and should not.

The first is a steller navy which protects ships and planets from pirates. They are quite powerful. The second is a trading corp similar to starbound, or stellercorp, all their ships are frieghters and unarmed. They are both allied aswell.

So why then does the steller Navy always see the need to attack their own ally the unarmed trading corp.

Is it a problem with the dude resource? I have thouroughly gone through both of their Govt resources, and everyone else, to make sure there are no ally and ememy conflicts, so I dont think the problem lies there...

Please What can I do???

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