In Act Two, we see Elizabeth's conflict with her husband, John. He asks if she is sad again, and "she doesn't want friction, yet she must" say,
You come so late I thought you'd gone to Salem this afternoon.
She seems to still suspect him of having ulterior motives for going to Salem. Elizabeth is somewhat justified in her suspicion since John shortly reveals that he spoke with Abigail, his former lover, alone, when he'd led Elizabeth to believe that he was never alone with the girl.
We also see evidence of Elizabeth's conflict with her employee, Mary Warren, in Act Two. Even though John has forbidden Mary to go into the courts in Salem anymore, Elizabeth feels she could not stop her. She says,
I couldn't stop her [....]. She frightened all my strength away.
Despite their age difference, and the fact that Mary is employed by the Proctors, Elizabeth still felt overpowered by Mary, especially given how powerful the court has become in town. Mary claims to be an official of the court, and Elizabeth is afraid to interfere, it seems, though she's also trying to obey her husband.
Then, in Act Four, we see evidence of Elizabeth's internal conflict, a conflict she's had much time to mull over during her three months in jail for witchcraft. When John asks her forgiveness again, she says,
I have read my heart this three month, John. I have sins of my own to count. It needs a cold wife to prompt lechery [....]. John, I counted myself so plain, so poorly made, no honest love could come to me! Suspicion kissed you when I did; I never knew how I should say my love. It were a cold house I kept!
Elizabeth has felt conflicted by her love for John and her simultaneous distrust of that love. It sounds like low self-esteem has caused her to doubt his love since its beginning, and she blames herself and her behavior for John's infidelity. Only now can she really put that conflict into words.