Well, I know you’re not supposed to use their cage as a place for a “timeout” because they are supposed to associate it with safety.
My Pepper got the bedroom door gate off the hinge and came right in. I poked her out with a stick, and then pressed my hand on top of her head and gently pushed her head to the floor and held it for a few seconds. It’s one of the things that dominant bunnies do to “discipline” others.
She did it again, so this time I THUMPED (stamped my foot), again pushed her head down, and then turned my back on her. I generally ignored her for most of the day.
In the evening, as she sat on her bookshelf (one of the two places She will sit when she wants grooms) I relented and gave her a good round of skritches. She sat very quietly, even when I rested my hand lightly on her back. She KNOWS she screwed up but was glad I forgave her.
I’ve had really good results with these techniques, from the Language of Lagomorphs website. You just need to “talk” to her in ways she understands.