the beggining of the song was, "I know that you lied to me". So my guess is that she means that Tidus lied to her about that "I promise i'll come to you when I whistle" promise.
I believe at that point in the story where Tidus told Yuna about the "whistle" promise, he was not aware that he was (SPOILER) just a dream . So technically, he didn't lie to her. He trully believed that he was real and would come back to her. It was only later that he found out the truth.

Besides, Yuna & the others lied to Tidus too. Or rather, they hid the truth from him. No one (SPOILER) told him that Yuna was supposed to die at the end of her pilgrimage. It was only when Rikku told him, then he knew

I think the lyrics are really about Yuna/Lenne's anguish about having their love taken away from them suddenly by fate. When you've lost someone you love very much, you naturally get upset and tend to blame them. ( eg, "How COULD you??!! How could you leave me?, etc, etc)