I think you should double-check everything, since they are perfectly fine. The only things that can make that message appear is if they are of the same gender, they are of different egg groups or they are in the Undiscovered egg group. The latter two don't apply, both of them are in Water 1 and Water 3 so that shouldn't be a problem. Are you sure they are the same gender? Are you sure that's actually the message you're getting...?