I think everyone is reading a bit too much into this one.

When Kate put the handcufs on to start with, she had them VERY loose. Benry obviously noticed, or mentally remembered Kates past and realized she may easily know how to get out of handcufs, so asked her to tighten them. If you watch that scene, Kate makes them very tight (so the metal was touching her wrists on all sides...like a really tight bracelet).

ANYWAY, obviously it is in Kate's nature to try to escape...to get out of there. In my mind, the marks came from her simply trying to get her wrists out of them on the walk to the cage from the beach. Twisting your wrists hard against metal like that would obviously cause some sort of marks to appear. And i'm guessing, if you're trying to escape being held captive, you would struggle as hard as you possibly could to get out.

There are no other marks (that i can see) that would suggest any other physical contact or struggle between Kate and any member of the Others/Dharma/whoever they are. This is simply Kate's doing.