Alternate version
 
Well, it seems that your visit didn’t just make Fluttershy happy, but her “babies” as well.
 
Yeah, she decided to call them her “babies”, for Twilight’s dismay. As far as you know, Fluttershy got infested my some kind of parasistic creature from the Everfree Forest.
 
The parasites are not harmful for their’s host’s body but, when they finds a creature that they can call home, they start starts breeding without control, filling their host until they can’t fit anymore.
 
Knowing this, Fluttershy decided to let them be, as long they don’t try to infect other ponies, even if that means she will look like a pregnant body as long as they stay in her. She doesn’t seem to mind having them squirming inside her womb, she even enjoys it as you can judge by looking at her face.