Actually, this seems like a potentially interesting feature to me. Instead of rushing to "fix" it, why don't you playtest it instead?
It could represent a convoy of ships "supporting" the one ship that needs to be delivered to its destination. I'm not sure if that physically makes sense, because I don't know much about faster-than-light physics. But from a gameplay standpoint, this sounds like a potentially interesting feature.
It would be a little hard to exploit this terribly, because the trailing ships would be left behind. And you couldn't go completely nuts with it, because you'd be limited by the maximum fleet size.
I suppose you could either make a line of cheap ships with only an engine (it wouldn't help to make them faster than the "payload" ship.) Then you could leave them in place to act as a "fireman's brigade" to send additional warships. (Either fill in the gap at the start of the line to extend it, or maybe have them each move back one jump to keep the line in place.)
Or you could use a bunch of warships to "leapfrog" each other to the destination. They wouldn't all arrive at the same time, but it would be darned hard to pick them off before they re-integrated.
You could program the AI to do this at high "intelligence" levels. I think it could be an interesting surprise for a player. It would be fun to see how long it takes a skillful player to figure out he needs to disrupt the supply chain.
I think I'll give it a try this week, anyway. Call me an "exploiter" if you want, I don't really care all that much as long as I'm having fun doing it!
Even if you do decide to disable this, how about considering adding a new tech (maybe a branch off the logistics tree) that re-enables this ability?
