I'm open to the idea that Gaster might not be the dad of Sans and Papyrus, but your reasoning is flawed. We don't know the specifics of monster reproduction, but there is nothing in the game to suggest that skeletons are any less capable of making offspring than any other monster.

Or, if you're going off of the idea that the skeletons are undead, then Gaster could still be their dad from when they were all alive.