The scene in the mirrored carousel room has some genuinely disturbing shots of Nell/Carolyn wherein she has lost all sense of who she is, and her own face is replaced in the mirror by Carolyn's. Both Carolyn seeming happy to be given flesh once more and her stretched, distorted face a few moments later count as a Nightmare Face.
In general, Nell's behavior. While Nell may not behave as unhinged as in the original, her Dissonant Serenity in the face of everything that happens around her can be quite unsettling.
The carved cherubs in the bedroom.
The whole story of Hugh Crain's children and their deaths. It is quite unsettling to see how insane and twisted Crain is.
Mary being injured by the harpischord and the kind of scars, disfigurement or other injuries she might face are not for the squeamish. Even if we don't see much, it's pretty horrifying to hear her scream in pain.
Luke's death is this...even though it also comes off as a bit silly.