@Background Pony #9236  
Finally, someone notices.

The differences in appearance are all kinda camera mishaps. A lot of times pictures are way off from what’s actually there. Sure, the cutie marks are because they’re tied to identity, and the clones don’t have the same personality as the originals, but the other stuff is camera stuff. The eyes being more solid and saturated (at least in Twi’s case) could be from the camera flashing in their eyes, and the faded colors could be that weird thing where flashes make the room seem darker than it is. The colors in Twi & RD’s hair could be a mirror effect too. Yeah, it’s a stretch, especially considering the actual pictures aren’t like that, and I doubt the animators put that much thought into it, but it’s fun to theorize.

@Background Pony #0C7E  
At least AJ’s eyes are still green. Evil Twi’s eyes are… more wrong.

I also noticed that AJ eye colors are the only directly wrong since she was the only one who Chrysalis didn’t took a shot of her eyes (She closed them in the photo)

Of course an altered mark goes un-noticed, because nopony would want to admit to staring at booty.
 
I immediately noticed the green apples because I can never forget the silly pony’s beautiful flank.

I love how RD’s is just… upside down xD

No mention of AJ’s also-green hair ties?

Don’t know why, but I want to spank anti-Applejack’s flank

At first, I thought Evil!Applejack’s cutie mark is a trio of pears.

RD’s mane colors are also reordered.

@Background Pony #BF51  
Safe assumption. Cutie marks are intimately tied to a pony’s identity–a graphical representation of their “soul”, you might say. Queen Chrysalis’s evil magic couldn’t make perfect copies of the Mane Six, so their cutie marks were the first obvious imperfections.

And now every time I see an image here of the mane 6 where their cutie mark is off in some way, I’m going to assume it’s an evil clone.

Here’s another interesting difference. Mean Twilight’s hair stripes. The normal Twi has the light purple one to the left of the pinkish one. Mean Twi’s are pink first and light purple to the right.
 
And speaking of tag semantics, “Mean Twilight” is a much better tag than “Evil Twilight”. Just my opinion.

Aha! Pinkie’s yellow balloon is usually higher than the blue ones.
 
Twilight’s normal cutie mark has the magenta six pointed star superimposed over a white six pointed star. Mean Twi’s inner star is also magenta.

@Hopeful_Ink_Hoof  
Actually the white stars are the same. It’s just that the big pink star in the middle is supposed to have 6 white points and 6 pink ones, instead of all 12 pink.

@Background Pony #EBFB
 
The same way they didn’t notice that the evil six were faded.

@Background Pony #6839  
Pinkie’s are reversed in height, the blue balloons are higher up than the yellow one.

@Background Pony #6839  
Evil Pinkie’s CM has inverted colors, Evil Twilight’s doesn’t have the white star behind the main one.
 
I just noticed that Evil AJ’s hair ties are the wrong color too.

I am thinking this can only be seen by us, the viewers. And that the ponies see them as normal.

@Background Pony #6839  
Actually, Twilight’s and Pinkie’s are changed. The white stars around Twilight’s are mirrored, and regular Pinkie Pie’s has the yellow balloon above the blue ones.

I don’t get why only AJ, Shy and Rarity have different colours, RDs up site down and Pinkies and Twis haven’t changed

Subtle