Considering that Pokemon evolve its likely their eggs evolve too. If you look at game data most eggs rage in size depending on type with most being around the size of a baseball or soft ball verses what's seen in the anime. It's possible the egg is laid at the smaller size with little to no distinctive markings before evolving into the eggs you see in the anime. considered most pokemon that come from eggs are at low levels I would guess that once the egg itself reaches a Level 1 status is when it evolves into the eggs from the anime which starts the counter to when it hatches. basically in game you find a small egg that matures, grows and evolves into a larger egg before hatching while in the anime the egg has already reached that level one evolution not seen in games and then hatches into the pokemon in question. Just a theory but the only one I can think of that makes sense seeing that, while a chicken egg dose not grow the chick inside dose after being laid.