It's possible the cancer had spread to her brain and that was the one that killed her.
Don't know, just saying it is not unusual for a secondary site to be the one that ends a life. Actually, she probably had many sites where the cancer had spread.
If I remember correctly, she had cancer years ago, before JonBenets death, and it was brain cancer having spread from breast cancer.
I'm sure you're right about the cancer spreading, rarely does cancer not spread to other areas/organs.