that sunset was a changeling hence the green magic

@Binkyt11  
You were almost right  
>>1451881t (merged)

@blacksunset  
this, probably too similar

@Alexlayer
 
Yeah, it keeps things consistent with her mindreading/empathy magic aura.

Well, for what’s worth, I like the new red.

@ice1517  
When it turns yellow, you better speed the fuck up lad.

@Binkyt11  
So it takes about 3-4 years to go form start to stop?
 
Damn, traffic must be torture.

@Ebalosus  
That’s why I mentioned the 99%  
For every one that doesn’t match their eye color you could name a plethora more that do match.

@Background Pony #04F9
 
It’s not really a mistake. But it does throw wrenches into people’s headcanons.

Sunset’s magic has been red since we’ve seen it in Rainbow Rocks. Technically this isn’t the first time this mistake occurred.

@Binkyt11
 
You win the internet

I have the perfect explanation for this… Sunset’s magic is just a really long traffic light.

@Ebalosus  
True enough, I always had the rule being the unicorn Iris which matches “most” of the time, but there are so many inconsistencies we can’t really pin point a rule.

@Ebalosus
 
And they have changed the color of other characters in the past.
 
Since both characters had auras of the same color, it makes more sense to differentiate by changing Sunset who has changed a lot since EQG, and now has an element of her own.

Sunset’s Magics Are Not RED!!! You all continue to make me most Angry with this Most Criminal Of Changes In History EVER!!!

@Alex
 
The rules are a bit vague AFAIC, because it’s a bit inconsistent:
 
-Trixie: purple eyes, purple magic, blue cutie mark  
-Celestia: purple eyes, yellow magic, yellow cutie mark  
-Minuette: blue eyes, yellow magic, yellow cutie mark

Yeah I would chalk this up to a mistake on the animator’s part. Pony magic is generally supposed to be the same color as their eyes. There are a few exceptions to this but when 99% of the ponies in equestria adhere to that rule I think it’s pretty safe to say that that’s the rule. Her magic was the correct color in the original EQG but I suppose they forgot about it in this.

@Background Pony #FDBE
 
Or more likely: the gag wouldn’t have worked given that SS’s old magic aura colour and SG’s magic aura colour are nigh the same.
 
After thinking about it for a while, I think a more suitable colour for SS’s magic aura would’ve been white. I’m fine with red, though think it’s a bit subdued due to her mane colour. Would’ve preferred the old light green, because I’m a fan of that colour. White would’ve made more sense since it stands out more, at least IMHO.

@Ebalosus  
Could be a Physical abnormality,Like most Unicorn magic matches their casters eye colors but there a few who for whatever reason a genetic,mental or magical impairment means their magic is a random color. It’s not dangerous or a handicap,rather it’s like being left handed or something.

@Background Pony #FDBE  
Well, I guess it’s easy to explain everything if you just go “THEY DIDN’T CARE”

@PonyPon  
Or they didnt care

@Princess Trixie vi Equestria
 
I thought it had to do with the colour of their cutie mark. Case-in-point Minuette:
 

 
But then again, it’s not like the show’s been super-consistent about things like this.

@PonyPon
 
Still more than we ever got for Twilight’s change.

I like to think, element or no, it’s because she’s been through changes.

@Slaccented