this isn't a glitch certain pokemon can mate with each other when put into the daycare the pokemon which is female (evidently the bagon) determines the pokemons species whereas the male pokemon determines other attributes such as the moves that it has when hatched and the nature(possibly) etc. Anyway if u want more info i suggest going to a site like www.gamefaqs.com and there should be a guide on the faqs page for poklemon ruby about this breeding thing. Don't giveup if u are confused by it because so was i to begn with.

Hope this helps!