After a bit of thought I think the only realistic posibilites are the baby is either Jin's or the pregnancy test gave a false reading.
Jin and Sun were at it the night he got back as indicated by Hurley's "Nice one duuuuuuuuude" thumbs up. At the time of The Whole Truth a few days had passed, Jack clearly said the test could come up with a false negative within the first week but not a false positive. Could this test have been tampered with? It would certainly make Jack look bad and perhaps lose it again if he had given this impossible hope to Jin and Sun.
Where did the pregnency test come from? I can only assume it was already in the hatch as its unlikely that it was on the plane. This begs the question, why would there be a pregnency test in the hatch in the first place?
I DO think Sun slept with Jae (her English teacher / ex "boyfriend"
which is why she looked so guilty and was shocked to learn she was not the one with faulty equipment ("You're telling me this now?"
but I dont think he got her pregnant.