The big one to me is voyeurism. Many a supposedly well-intentioned story where rape is an element is completely undone and revealed as a lie by the deliberate attempt to make the viewer feel a vicarious thrill for the victimizer, not the victim.
Second, remember that the victim is a human being. Many, many, maybe even most, stories with rape prominently figured tend to put the following narrative on everyone but the victim, who often is referred to from then on as:
1) A victim partially to blame for their own poor judgment
2) A martyred, defiled saint, or
3) that character who was in the story for a rape scene and now doesn’t seem to exist anymore.
Those are the two big ones. And it wouldn’t hurt to be well aware of the long history of rape mythology and make a real effort to avoid those tropes.