You can only cut Kana's rope if the Native Boss is still alive (and you're playing the Male MC and using a Knife/Blood Knife/Kodachi). If you killed him, Kana also gets strangled to death (until the Native Boss' next respawn), and clicking the rope will only play the animation and waste durability without actually cutting her down.
It can be hard to cut the rope while the Boss is moving around in combat. To make things easier for you, either sneak up on the boss from behind him (only after he respawned on save and reload; he's forced to aggro you on your first encounter), or pause the game with Esc so you can click the rope more easily.