Bugs:
The planet station with the restaurant (name escapes me) has spare ship parts for sale cheaper than you can sell them back... very handy for quick money making but maybe a bug?
The restaurant mission never allowed me to deliver the ten requested carapaces despite having them... I tried bought ones, hunted ones, ones from the shop next door (!?) - none worked.
I sold the map of Lost Wisdom so I don't know what I should have done with that and there seemed to be no way to reacquire one even though there was the option to sell it too... the only thing I found at the station was a hand telescope...
The Kiwiman mission doesn't complete when you give the Carapaces, neither are the carapaces removed from inventory (bug you get the doppies and reputation)... useful but bugged I'd guess!
The Rebel base didn't seem to turn up when I got the mission to go there from the guy in prison (I already had enough reputation) so I have to follow the Federation questline until it did and then ignore it and continue with the rebel one...
I'm sure there were other things too (maybe a mission that didn't take away Ship parts I supposedly donated?) but I have forgotten them right now... I'll write a message when I play it through again if I can find them! :)