The Penguin Books edition of Arthur Miller's The Crucible includes Act II scene two in the book, but it places the scene in an appendix. The note at the end of Act II says that scene two was part of the original 1959 theatrical production of the play but, at the author's request, was removed from all reading copies of the text until 1971.
The scene has only two characters: John Proctor and Abigail Williams. They meet in the forest one night after Elizabeth has been arrested, and Proctor is the one who requested the meeting. Abigail is a rather pathetic figure, worn out and sore from all the places she claims the "witches" she has accused, including Elizabeth, have poked her and stuck her with sharp objects.
Despite her condition, Abigail is confident that Proctor will want her back one day, now that Elizabeth is out of the way. She says, "Oh, John, I will make you such a wife when the world is white again." Proctor is unmoved, saying he only called her here to inform her of his intention to tell the judge everything in the courtroom tomorrow. He is warning her, he says, in order to "give [her] all good time to think on what to do to save" herself. Neither of them change their positions by the end of the scene, and Abigail's last words are that she will save him at the trial tomorrow.
There are several possible reasons why this scene is generally omitted in theater productions and read separately in classrooms. First, the scene depicts Abigail as a sympathetic figure, a young girl who has come to believe her own lies and is even hurting herself in her delusions. In reality, Abigail is a schemer and a liar, intent on doing nothing except what benefits her. Miller says she has "an endless capacity for dissembling," and she has consistently demonstrated that ability. Proctor must take blame for the affair; however, what happens after that should engender no sympathy in the audience, so the play is better without this scene.
Second, Proctor looks weak and unresolved when he offers Abigail the chance to save herself. He has said to both Elizabeth and Abigail that he will have nothing to do with the girl, yet he invites her alone into the forest at night to offer her a chance to save herself. It looks like weakness and perhaps lingering love on Proctor's part, so the scene is better off in the appendix.
Finally, it is a digression in the plot. At the end of Act II scene one, John is resolved to do what he must to save Elizabeth, and he is determined that Mary Warren will tell the court the truth. His announcement to Abigail that he intends to tell the court everything about her is a digression and a distraction, especially considering the arguments above.
In short, after seeing it on the stage (and presumably receiving mixed or negative feedback from his audiences), Miller must have recognized that this scene did not make his work stronger, which is why he chose to eliminate it from any subsequent printings of the play.