Seska assumed it was chakotay's baby but she was probably already pregnant with the Kullah's baby when she tried to impregnate herself
Up until that point it had been Chakotay's, the only mention of Kullah was she'd slept with him so he'd think it was his until it was born. It felt like a last second change because someone balked at that idea.
Having looked at the behind the scenes, that's exactly what happened. It was written as Chakotay was the father. Piller left, and they changed it, and quite a lot of things that was planned for part 2.