These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: My Little Pony Friendship Is Magic S 3 E 3 Too Many Pinkie Pies
As mentioned below, stories about multiple Pinkies already exist but the Mirror Pool now gives fans a canon method of creating clones.
The mystery surrounding its existence and the accompanying book that was sealed away at the library.
The idea of the remaining Pinkie being a clone or one of the clones getting missed in the roundup.
Fridge Horror: All over the place. Twilight eliminated a few Pinkie clones just for sneezing or scratching her nose. Imagine what would have happened if the real Pinkie didn't have the intense focus she demonstrated here...
And this one. "Pinkie's gone and broke [sic] the fourth wall again! She's multiplied herself to unimaginable numbers, and now Twilight Sparkle is the only one who can stop the rampaging horde of Party Ponies. Don't feel bad about putting them down though: They are only semi-intelligent copies of the real Pinkie Pie, who is nowhere to be found."
Also, fans had originally guessed that the Mane Six would clone themselves in order to better help with the wedding preparations in A CanterlotWedding based on the clone filled trailer. This was before we learned anything about the Changelings.
A good chunk of the fandom seems to have decided that since Fancy Pants was in Ponyville, this obviously means he was doing something with Rarity that cannot be shown on children's television. Supporting this, Rarity was dressed to the nines for no clear reason, and it seems odd that a Canterlot noble seems to be just hanging out in Ponyville....
The way Noteworthy and Golden Harvest were smiling and waving at each other from their windows at one point could also be seen as something of a background pony Ship Tease.