Lillipup is kind of shoehorned after it as well, especially being such an old card. Without any knowledge of how they plan things, I'd guess that #51 and #52 were supposed to be original releases of these boxes, and the Emerging Challenges Box was a last minute thrown together thing that had the promo just take any available slot. (Given by how no-one seemed to know about it until it was at retail that seems likely either way)
Or maybe box Keldeo was supposed to be #51 and mistakenly given #60 which at the time was ridiculously far ahead, either way Crobat probably was meant to be later, but he was (luckily) given the task of filling the hole.