I think here's always been height differences between the ponies.

[GuillermoGage 246]

I've been looking at renders from official merchandise in which ponies are side-by side , and despite the insistnce that the Mane 6 are all the exact same body base, I've noticed that Pinkie Pie is noticeably shorter than twilight, even before Twilight became an alicorn. I've paused during episodes when at least two characters are lined up and the same distance from the foreground, and I have noticed height differences. Twilight Sparkle, Applejack, and Rarity are generally taller than Pinkie Pie and Rainbow Dash. I haven't taken a look at Fluttershy yet.

 

It seems like there is a subtly difference. This is called Divergent Character Evolution.

 

A similar comfirmed phenomenon is that the Cutie Mark Crusaders do look a little taller in later more recent episodes, from Season 1 to 3 and beyond. I haven't noticed one being taller than the other, but theere are subtle changes.

 

It really looks to me that Twilie has always been taller than at least some of the others in the Mane 6.

[Treble Bolt 1,122]

I think there's a lot of other's noticing this, especially since Twilight's ascension. I think overall, Pinkie's mane has deceived us all!

I am not sure why, but Applejack seems taller than Rainbow Dash as I noticed in Fall Whether Friends...but maybe it's just her hat...

[Scootalove 10,684]

I've noticed it too, ever since Twilight's ascension she's gotten a bit taller than before. Applejack does look a bit taller than Rainbow Dash, must be the hat or she has grown lately.

[~Silver Essence~ 2,621]

Well, with age and experience, one does grow up a bit by height.

 

I too have noticed that, but even then, that's not really something TOO different from what we've seen.

[SparklingSwirls 21,263]

Well, I've only noticed Twilight being taller since her ascension, but I haven't compared the other ponies to each other. Maybe I'll try to watch for it.