SPOILER ALERT: HUGE SPOILERS, dude! I will be primary speaking about Fruits Basket and Nabari No Ou, both mangas and animes. And other things. But mainly that. If you haven't seen them, you shouldn't be reading this unless you like having endings spoiled.
So, what the hell?
When I read up on the manga of Nabari No Ou after finishing the anime, I discovered that Miharu really does go back and ERASE YOITE! I was stunned. The manga ending, in that case, is even worse than the anime ending. In the anime ending, Miharu doesn't erase Yoite, seals the Shinrabansho away inside of him, and happily lives out Yoite's last days with him until Yoite dies by disintegrating into fairy dust.
I. DON'T. UNDERSTAND.
The entire story revolves around Miharu learning to use the Shinrabansho to erase Yoite, so changing the ending... ? It's a risky business. That would change the future of all of the central characters. That's.... that's... ! SHOCKING! Frankly!
Don't get me wrong. I love exploring other possible endings - but by making them different between anime and manga, it's like WE as the reader have to decide which version we are accepting as 'real'. It sucks!
One other manga-to-anime f***-up would probably be Fruits Basket....
Let me just say, I love the manga to death. After hearing how the anime ended - how Akito isn't secretly female as she/he is in the manga - I didn't even want to watch it. That is what the ENTIRE story relies upon. Akito's irrational and terrifying behaviour stems from the way her father, mother and Shigure treated her, and that was influenced by the fact that she had to pose as male her whole life. But in the anime, 'she' is biologically male.
It really got to me because I love Akito as a character, and after the plot twist, she just gets better. So why, or why, did somebody decide that this change would be okay?!
Now let me think, I think the ending of the anime was something about the 'God' of the Zodiac - Akito - being possessed by death curse? Which has got to be, more or less, the worst thing I have ever heard.