So... I was jumping my fleet from one planet to another when suddenly it decided to stop. A little investigating revealed that my Sova carrier had disappeared, and its fighter craft were floating in space with the blue "returning to mothership" circle.
If I moused over the Sova in the taskbar, it showed a blue jump line from where it should have been (approximately) to the next planet. However, trying to zoom to that ship dropped me into the blackness of space, unable to so much as see the fight's star system. Only way to get back was to zoom to something else. Turning the whole fleet to "jump individually" let everyone else go, but my Sova is still lost in space, I guess. Ordering the Sova to move somewhere else did nothing, but ordering it to stop at least freed its bomber squadrons to fight in-system. Ordering any squadron to dock just made them stop dead in space.
This is a horrible bug report, but I do not know how to describe this one any better.