The scene that has lingered in my memory for a few days...(spoiler)
The scene at the beginning where the Witch kills the baby and then starts doing...stuff, with it. That scene is disturbing. It also is a stylised scene that I have seen rarely in horror films. Usually a scene like this would end in a jump scare, and normally would come at the end of the movie too. So it was strange seeing at the beginning, and just having bizarre and disturbing imagery as opposed to jump scares.
I'm still not really sure what the Witch was doing in that scene, apart from killing the baby (which is disturbing enough).
So while the rest of the film has dissipated from my mind for the most part, this one lingers.