Sorry dude, there just isn't any possible way for this to happen. Even in real life, the only living things that can reproduce by themselves are cells and flowers.
There's a way to override the Day Care system in Ruby and Sapphire, meaning that if you put two breedable Pokemon togethter, and walk the amount of steps it takes for them to lay more than one egg, then you can talk to the Day Care Man and get one of the eggs, and quickly return to the Dare Care Lady and pick up your Pokemon while there is still an egg waiting to be picked up. Putting two new breedable Pokemon together, and picking up the older egg can be confusing at times.
Sorry if I explained that in a complicated way, but that is a definite candidate for what happened. It happened to me once, when I was breeding Treecko, and took back my Sceptile and Salamence, and replaced them with Pichu and Clefairy. I was so freaked out to get an egg back that hatched another Treecko.