When Eleanor is in the Greenhouse in a daze, as she ascends to the plank, she's barefoot. But, as they cut away to Dr. Marrow and back to her standing there, she's wearing winter boots, and then they disappear again.
I watched this scene carefully when I watched the movie and I can honestly say that I didn't see her wearing boots. They do cut back and fourth but each time I looked closely and didn't see anything.