I was out of fuel and requested assistance from a Heavy Shuttle trading back and forth between Earth and Mars. It agreed (for free) but then turned hostile and carried on its merry way. Whenever it stopped at a planet it would turn blue again but as soon it left it was back to red.

That sounds mildly out of the ordinary. No ideas for what the problem is.

Maybe it's your legal rating.

Do you have the Salvaging Goverments plug in? That might do it.

Nope, no plugs that would affect this and I have a high enough status. I'm guessing it's just some weird bug. Like in EVO if you jumped out of a system while your escorts still had fighters launched the fighters would get angry.

I've had this problem before, no plugs used.

Maybe it has something to do with them having the 'scoop asteroids' field checked. Why don't you try asking an asteroid miner to give you fuel and see if they do the same thing?

Oh and by the way if that happened to me I'd turn on all my flashy guns and blow 'em outta the water.

Yes I know it has something to do with that, that's what an economy-at-work ship is. It's a special feature of Nova but has this odd side-effect. It didn't attack me, just turned hostile so I left it alone.

I have a similar problem where sometimes when I arrive in a Federation system, there will be a Federation Viper that will instantly be angry at me and then jump out of the system. At times, this has set off chain reactions that get all Federation ships angry at me, or calls in defense fleets (though usually it'll just be the one Viper, and any other Fed ship in the system will just act normal.)