Are you talking about the very first mission (the pilot) or the third mission (episode 1 of season 1, named "33")?

Btw having the same issue. I'll try to describe it in as much detail as possible.

In the second jump (jump 239) you are asked to "move" the fleet to a given position (I assume "move" actually means "jump").
Within the 1 min countdown I jump all civilian ships one after the other. I select all remaining ships and keep hitting J until the plotting overlay for jumps is displayed. Then I click and the ships that can now jump, jump. This continues until the countdown expires. At this point, only the "Botanical Liner" is still there (I may be messing up the name, I'm writing from memory), which then jumps after a few seconds. In the meantime, I have sent the Viper out. As soon as the Botanical Liner is gone, I set the Galactica's landing command to "Docked", draw a frame around the BSG and press D to order the fighters to dock with the next carrier. The fighters dock, and now everything should be ready for the Galactica to jump, but I can't make it jump. The mission ends with her destruction.

Its likely one or two of the civilian ships are just outsize the destination volume of where the ships are meat to go. Double check they aren't round the edges, i'll make it a little bit bigger for the next update :)

Originally posted by Bings:

i'll make it a little bit bigger for the next update :)

Thanks, maybe that helps.
I'll test it with another approach: Waiting for the last civ ship to be able to jump and then let them jump as one group. That should in theory keep them as close to one another as possible.

Ok the trigger box really needs to be expanded. After they jumped I had to reorganise them closer to the destination point so Galactica's FTL would become available.