did sun have an affair with her english teacher or is it a fact that she doesn't know how she got pregnant because in the last episode to show so far ("the whole truth") she looked kind of guilty yet confused when she was hugging jin after she had told him about the fact that she is pregnant and then jin said it must be a miracle.

If it's a true fact that she doesn't know how she can be pregnant than this strengthens two theories about the show. The one were they were taken from the plane then placed in some sort of sleep and then when the group or force was finished with them, he placed them on the beache and placed sheds of plane on the coast and dead bodies in the water to actually look like the crashed, to the force or group could see how they would live primitively. (Sorry that I can't credit who ever came up with this theory in the first place, I've heard it from too many people.)

The other theory that this could strengthen is the "The Black Box Theory" by JediToad. Maybe in sun's memory she thought that since jin wanted one so he wouldn't have to do the work her father assigns him and would go easy on him that she would make jin happy. When jin got mad that she was in the garden because it was dangerous it triggered a memory of the same 'emotional damage' (the memory of the point were she found out she wasn't pregnant.) So sun wanted to make it all better so she made herself think she was pregnant (subconciously) and in the end she becomes pregnant because the mind is "rewriting itself".