I am sorry to hear your hatched Manaphy did not make it. I also hatched mine from the pokemon ranger game it transferred easily enough.Its a shame for anyone who bread or caught their pokemon in game if they don't make it I. Have been playing since red/blue have kept all pokemon since ruby/saphire I transfered about 1600 pokemon yesterday no problems and for me they are all hatched or caught in game or events I attended accept for about 2 to 3 that I traded for. I would be upset if I lost my older pokemon so I hope that there is a way for you guys to get your hatched/caught pokemon.
For the people that hack/RNG if they don't get through oh well just try to recreate them a little more accurate as my understanding is most can make it as long as properly made and the RNG I don't see any reason they would not make it.