Lately, I've been using the set rally point option on my homeworld to make it so all ships that are built all move to my flagship, which works great! I never have to worry about rallying together my fleet every time I build something new.

But something weird happened when I build a Trade center by my homeworld. It was the first trade center to be constructed by me, so that might be part of it too. Once it started producing trade ships, the trade ships would immediately begin warping to the location of my flagship and puppy-dog it around wherever it went. Because you can't directly control trade ships, there was nothing I could do to send them elsewhere.

Eventually I had to set my rally point to somewhere inside my homeworld space and scuttle all the trade ships so that new ones would be built, at which time they finally started picking up goods and beginning their trade routes. All through this, I did have trade agreements with other races, so it's not like my trade ships didn't have a job to do.