[dogscoff]

Wierd. The only non-bug answer I can think of (although it's highly unlikely) is that the enemy ship came through the wp cloaked, thus avoiding combat, and then either decloaked (maybe ran out of supplies) or that you happened to build a ship in that system on the same turn with scanners capable of penetrating his cloak.

Like I say, possibly possible, but highly unlikely.

If you can remember what class of ship it was, have a look at it's design (designs / enemy designs) and see if it had stealth armour or a cloaking device.