I had a Rapture Battlecruiser get stuck between two wormholes on the Implosion large scenario.
It seems like it never went in to phase space but just tried to cross the distance by regular flight...
I had previously explored the wormhole and sent my fleet through. Then I set a capship factory to produce the rapture and set the rallyingpoint to a capship in the fleet. Then when I looked for the finished ship later I discovered that it was stuck approx 1/5 of the way between the two wormholes.
Hope this helps. I seem to have deleted the replays and the save:-(