Sounds like the classic "I reclaimed a unit on a planet with an astro regenerator train" bug. The teleport elsewhere and respawn happens before the ship ownership is transfered to the reclaiming player. (This also impacts regenerations by regenerator golems, but as they teleport the ship to their own position, it's not as annoying)
A similar thing happens to regeneration and units with tractor beams (if units X is tractoring unit Y, X dies but gets regenerated, it brings Y along to where it gets regenerated) and eating units (same as previous, but replace tractoring with swallowed)
http://www.arcengames.com/mantisbt/view.php?id=3387 (which is about zombie reclamation, but I posted in the comments that this also effects normal reclamation)
http://www.arcengames.com/mantisbt/view.php?id=6639 (for the tractor and eating form of this bug)
EDIT: IMO, I would consider this a major bug if it wasn't for the fact the astro trains can be turned off, and regenerator golems in the hands of the AI are moderatley rare. In fact, this bug is the only reason I am keeping astro trains off.