Many Bronies I’ve seen think its signifying a new ally joining the Mane Six.
 
If you’re wondering the current candidate for the believed new friend search Sunset Shimmer on here, she’s believed to be a new ally since she’s a Unicorn and appears in a toy set with the only other ponies in it being Mane Six members.

She has 5 stars in her CM, because her actual destiny was to be the element of magic, the little stars representing her friends.  
That is what her cutiemark always stood for.  
It’s the elements of harmony.

Here’s what I think happened: Her actual cutie mark didn’t change, and it wasn’t supposed to. When she’s an alicorn, it’s still 5 small stars surrounding a big one (that one picture that has 6 stars is fake). They just copied that on her alicorn model, so it didn’t change. The reason why the huge cutie mark in the sky and some other incidents where it’s seen in some place other than her body had 6 stars, is probably animators who weren’t there from the beginning or never paid that much attention to how the cutie mark looked like. They had to redraw it for those scenes and just figured the number six makes sense or maybe it’s just more symmetrical or something. It would be nice to have that cleared up though.

@richfiles  
That has to be a lot of animation derps. The giant glowing cutiemark: 6 stars. Her banners, all 6 stars. Her cutiemark when seen in various latter scenes: 6 stars.
 
It looks like the 5-star ones are derps now.

Animation derp.  
Alicorn Twilight still has 5 white stars encircling the central star.

TWILIGHT YOU MUST FULFILL YOUR DESTINY AND GET YOUR 6TH STAR

@Rarity
 
OOOOOOOOOOHHHHHHHHHHH~  
I get it now!

@Background Pony
 
I guess she was the last of the mane 6 to fulfill her destiny. That’s why she used to have 5.

I don’t get it