You can clear the orders of specific civilian ships on the Shipping Lines window
Ah silly me, Thanks for that. The issue somehow resolved itself after creating the infrastructure but I'll keep that in mind for the future.
I have however had a different and VERY interesting bug. The population of Earth (my capital) has suddenly surrendered to me. For no reason, this as far as I can tell had no negative side effects other than the fact that every ship that was in orbit at the time is now in it's own TG (so I have to reattach them all :/). Here is an image of the log
http://i.imgur.com/Es671X8.jpg. Suddenly surrender.
I don't quite know what could have caused it, the two major things I can think of that I've done (I think) just 30 days before this are:
1. Disabled fuel refineries on Earth (no sorium).
2. Destroyed the Mars "colony" (it was empty, no resources only had it there for the geology team).
Never happened before. It also happened 24 years into game time if that's of any significance.
EDIT: As it turns out there were losses. I lost 3 terraforming ships that apparently had the bad luck of coming out of the shipyards as the "surrender" happened, apparently this lead to their disappearance. I also gained a civilian ship that was in orbit.
EDIT2: Aditionally the military vessels in orbit lost their 100% TF training and are all back to 0