Continuity mistake: When Junior goes to fire Tulip she says it's her birthday. We then see Nate write a letter asking for a baby brother. In the movie the sun sets twice before the letter gets to Stork mountain. However, when Tulip receives her letter she is celebrating her birthday and after the baby is created she realises they share the same birthday.
Continuity mistake: When Jasper takes Tulip to meet her family, Tulip gives Jasper her iPhone so he can take a video of her. After Tulip hesitates to ring the doorbell and walks away, Jasper still has her iPhone since she never took it back from him. However, after Tulip finds Junior in Hunter's trap, she uses her iPhone to order and return a package. (01:05:05 - 01:10:10)
Chosen answer: Hunter had allowed the penguins to take care of the baby, and will then be returned to the human world when she is an adult. The penguins were taking the baby back to their home to raise it.
Casual Person