The first show stop happened fairly early in act 1, I believe it was a scene with Jude and Brother Luke. The second show stop was in act 2 during a scene with Dr Traylor. The characters of Brother Luke, Dr Traylor, and Caleb are all played by the same actor and he was the one who called for the show to be stopped both times when it became clear someone in the audience wasn't feeling well.
Sorry I couldn't be more specific but the play has a very non-linear structure and deliberately blends a lot of Jude's traumatic memories together so it's quite hard to remember some of the details.