I've run across a few small items, only two of which occurs to me now.
1. I had ended and restarted a game, and when I restarted, my trade routes were still listed from my previous game. I had not restarted Gal Civ, but just went back to main menu and started a new empire. I wasn't receiving money from the routes, and when I would research a tech which gave me an additional route, say #3, the route previously listed under #3 (from the previous game) would disappear, allowing me to add one, so it didn't cause any problems.
2. Another empire's trade route had been destroyed, but a small trade ship from that route didn't disappear, it just sat below one of my systems. It was annoying since this system was my biggest military producer, and when I would take a ship out of orbit, it would pop up over this trade ship, not allowing me to click directly on it to select it. When I did click on my ship (on top of this trade ship), it would just come up with a description of the trade ship, and never mine. I would have to go to the ship list and select it from there to move it. It did disappear when I allied with the civ who orig. controlled it. Strange. Maybe they were going for an "annoyance" victory, where I would get so annoyed and just start another game!
~SDC~