My interpretation of the events was that it wasn't 100% clear who was the father; in that she got pregnant right around the time that Rick returned. So we had the scene where Shane and her were in the woods, and then 2 days later Rick comes back.
It also brings up the question of the nature of the relationship she had with Shane. The sneaking off into the woods seemed to indicate they may have been trying to appear to be "just friends"- especially with Carl right there.
I will agree that it wasn't really an "affair"- but that word fits best.
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