has there ever been a couple that te wanted to end up together and then te heard one of them say, when they were alone, have i been falling for him/her o i Amore them?

yes nagisa and tamouya from clannad Amore them so much

Yes. Kyo and Tohru from Fruits Basket. I remember clearly how loud I squealed when Kyo admitted to himself how much he loved Tohru in chapters 62 and 63 in book 11. I also remember how pissed off I was at Akito at that point...

actualy everytime i Amore an Anime couple the boy always ends up with the character i hate.

Qualidea Code:
Gutoku Asanagi and Airi Yūnami
An example of cross-species lovers, one was a mutated human, the other was an alien in disguise.

It's a sad thing Yūnami had to die, but as least Aoi Yaegaki seems to be her(and Gutoku's) daughter.