I have this bug too. There seems to be no way to avoid it, and it seem to happen when ships jump by other ships still moving into position. You can order the "lost" fleet to jump to the planet they're supposed to go to again and they will right away, though.
Alternatively, you can just salvage them (Click the ship, click the orange/black bar at the bottom of the screen under the middle picture, or do shift + S) to regain some materials and fleet points.
While that's not a fix, it's at least something to make the game playable again.