@LightningBolt  
Yeah, I can’t picture Luna with black or white magic. It would probably clash with her coat color. The blue she has now looks pretty.

@mjangelvortex  
I dis some research, as I tend to do eye color or coat color for unicorn OCs or ponifications I do instead of CM color, and wanted to see if it made sens ein the show, and learned that the show follows no real rule to magic color of horn owners. :P Just usually CM color but sometimes eyes or something else if CM color looks bad. Imagine Luna with a black or white magic aura.

@LightningBolt  
It is very interesting. Now that the image has been merged, one of the commenters brought up that eye color is another common one. Luna seems to be one of the few whose magic doesn’t follow either of those rules. And Trixie had the standard mauve unicorn color that was common in season 1 but hers never changed.

@mjangelvortex  
A few days ago, I looked at the magic colors of most of the prolific unicorns and alicorn in the show, and while most followed CM color, some didn’t, like Sweetie Belle, Luna, and, uhh, Trixie I think. It’s pretty interesting.

@mjangelvortex  
It’s the very same reason her hair colors changed/desaturated post-Rainbow Rocks.

@Gian Song Yim  
And there you have it. It was a deliberate change. Red’s a more fitting color for her anyways in my opinion.

@mjangelvortex  
Season 1 didn’t have unique magic colors at all. That started in season 2 and has been pretty consistent.

I woudn’t really tag this as a continuity error. It seems to be a conscious retcon, especially if you consider that something similar happened to the other unicorns and alicorns in the series. A lot of the newer colors (but not all of them), tend to match their cutie marks whereas their older ones didn’t.
 
Twilight in season one:  

 
Twilight now:  

 
Celestia in season 1:  
 
(Her horn isn’t colored but look at the cup. It’s blue.)
 
Celestia now:  

I’m pretty sure they changed it in Mirror Magic because the color is virtually identical to Starlight’s. Sometimes it’s better to have continuity take a backseat to visual clarity.
 
No such excuse for the comics, though.

An innumerable amount of possible answers can explain this.  
The spell in question, surrounding atmosphere reacting, the unicorns physical state, sunset being exposed to the element of magic ,lazy artist etc..
 
Also neat observation about the season 2 change.

@cheezedoodle  
It’s because of the pendant! It has a red aura too. I think that actually makes sense now

@Background Pony Number 17  

 
Very light purple. A few still have it, like Trixie. But yes starting in season 2 they went with specific auras.

It’s like how SpongeBob looks on the surface.  
it changes every time

@Zharkaer  
If I recall, in Season 1 all unicorns had a sort of maroon magic aura. Individualized color auras didn’t come until Season 2.

Shimmer(Equestria One)/Sunset(Equestria Two)/S.S.( Equestria Nineteen)

This is easily explainable, so long as you know Power Rangers. Originally she was like the Green Ranger, who started out corrupted and evil but eventually became good thanks to the efforts of the other Rangers - her original aura reflected this. Eventually she matured from being the outsider Green Ranger into the leader colour of the Red Ranger, and her aura adjusted to match.

@cheezedoodle
 
That, and the fact that it’s never brought up in the narrative makes me wonder if the aura colour is more for the viewer’s convenience than something in the story. Kind of like how aliens speak english in most SF settings so the viewer don’t have to read subtitles. Case-in-point: The episode my avatar is from!

She’s evolving

It’s usually based their main cutie mark color or eye color. Some don’t follow the pattern though. Here’s a survey I just spent way too much time on:
 
Celestia: mark  
Luna: neither, it’s a light blue while her eyes are more turquoise.  
Twilight: mark  
Rarity: mark and eyes  
Starlight: eyes  
Sweetie Belle: eyes  
Cadance: mark  
Lyra: mark and eyes  
Shining armor: mark  
Trixie: lightest eye color  
Sunburst: cutie mark  
vinyl scratch: eyes  
Fancypants: mark  
Flim/Flam: Eyes and mark both have different shades of green but not a good match.  
Snails: cutie mark  
Snips: Unknown  
Moondancer: cutie mark (stars)  
“Fresh Coat:” eyes  
“Cayenne:” cutie mark (orange drops)  
“Leonardo Da Vinci:” no match  
“Carrot Bun:” cutie mark  
Sassy Saddles: gold, but she has orange eyes. Don’t know her cutie mark.  
Chrysalis: eyes  
Sea Swirl: eyes  
Lemon Hearts: eyes, but has also been shown with yellow magic  
“Starke Kragen”: no match  
Professor Flintheart: eyes

The stoplight theory was true!

‘facehoof’

She came over wearing her magic pendent that had red magic, that’s the only reason I can think of.

Consistency! Not just a big word!

@orbsah  
There’s that but she also was associated with red magic in RR, wasn’t she?