Good suggestions, but here comes the other problem:
I'm too lazy (and busy studying) for a new project
So I'd rather concentrate on finishing and polishing these two.
about the delivery service: It's called a goner delivery service, so I decided, the ships should still belong to the goners. Especially because if the delivery ships belong to the player, this makes an exploit possible. just stop them and then you have a new ship
about the found bug:
I just confirmed it. You can try yourself, if you want.
1. get a ship next to an undiscovered sector (I used a M5 Harpyie)
Btw: is it 'an M5' or 'a M5' ? It should be 'a M5' because the M is a consonant, but if I speak it out, I say "Em" so "An Em Five" would sound better. Which is correct? 
2. make the ship fly through the gate into that undiscovered sector
3. do NOT watch the ship on the sector map, just wait until it is in the new sector
4. check in universe map that the line, connecting the new sector to the old one is missing.
5. open the sector map of the new sector. Gate is there and voila, the line is also there.