Aren't the offspring always in the same evolutionary line as the mother, or did the breeding rules change? I've only played up to the third generation of Pokemon games, so I'm not entirely familiar with the gameplay mechanics beyond that.

no, you are correct. I guess the author just messed up with this small detail (or just couldn't come up with something better)

Or Ash is dense!

I thought the species was dependent on the sex of the baby? Male babies take after the dad, female babies after mother dearest.