This is why Rose only has one pig when you return to Outset Island later in the Game:

(Rose walks over to the pen where the three pigs are.)

Rose: Oh my goodness. It's a good thing that Link was able to get me these three pigs before he went with those pirates to save Aryll. I hope that one day, Link will return to see how these piggies have changed.

(Pink Pig bites Spotted Pig and starts burrowing into his flesh.)

Rose: No! Piggies!

(Black Pig bites Pink Pig and starts burrowing into his flesh.)

Rose: No! Piggies!

(Spotted Pig bites Black Pig and starts burrowing into his flesh.)

Rose: No! Piggies!

(While the three pigs are burrowing into each other's flesh, they begin to form a ball, suddenly, everything becomes silent.)

Rose: Piggies?

(The ball cracks open like an egg and a giant cowboy jumps out.)

Cowboy: Burrrrrrrrrrrrrrrrrr! I need cheese!

(Rose screams and runs off. The Cowboy begins to bang his head on Grandma's house. Grandma walks out.)

Grandma: (Calmly) Wa.

(The Cowboy stops banging his head and starts screaming uncontrollably. Abe runs to the Cowboy.)

Abe: Don't worry! I'll save you! (Throws a rupee at the Cowboy. It hits him in the eye. He stumbles and then falls into the pig pen, getting completely covered in mud.)

Cowboy: No! Mud! My weakness! (Turns into a big, black pig. Rose walks back to the pen.)

Rose: Piggy? (Sees the pig.) Piggy!

(Link arrives on the King of Red Lions. He gets off and walks to the pen.)

Rose: Hello Link. Look. The pig you brought me has grown up.

Link: But didn't I bring you three pigs?

Rose: No! You brought me ONE! BLACK! PIG!

Link:...

Rose: ONE!

Link: Okay.

Rose: Yes! Ahahahahahahahaha!

(The Pig vomits.)

The End