I'll attempt a complete guess at an in universe explanation.
The Game of Thrones wiki comments:
..."Arya" is pronounced "ARE - yuh". George R.R.
Martin himself has pointed out that a surprisingly large number of
people pronounce it incorrectly: it consists of two syllables, not
three (like how the "aria" of an opera is pronounced). Martin
explained: "I say it 'Are-ya', two syllables not three. Not
'are-ee-uh', not like an operatic thing, but 'Are-ya', very sharp. I
wanted something that was like a knife, that was a sharp and hard
sound, to be a contrast to the flowery 'Sansa'."
They refer to this video as their citation.
What I'm interested in is the last section - to be a contrast to the flowery Sansa. When we first meet Arya, she's the tomboy of Winterfell - but is still in Winterfell and being brought up as a lady. Much like Sansa is a very flowery name, perhaps Arya was encouraged to over pronounce her name to give it a more feminine, dainty feel.
However, with the loss of her family and with her becoming more and more wild, she fell back on her preferred, less sweet-sounding pronunciation and has stuck with it ever since!
As for an out of universe explanation... She's a young woman who has filmed all across the world, probably picking up various bits of regional dialect along the way. Perhaps she didn't know the real pronunciation to begin with. Perhaps George RR Martin had other things to concern himself with and didn't care. I can't find any interviews which suggest she deliberately change her pronunciation, so I'm going to say it's simply an incidental thing.