Hi,
The way to sort this is by getting her speyed. :wave:
It means her hormones will calm down and she will not feel the need to be territorial, mark her scent, lunge at you at random times, or attack things. It is also good for her health as it protects her against uterine cancer, which 80% of unspeyed females catch.
Also you can never fully litter train a unneutered rabbit.
Trust me- your rabbit will be much happier and healthier when she's speyed, and your problem, after a few weeks, will be gone!
I would also like to point out that even though she is let out, that cage is far too small for her. In the wild rabbits will run miles a day, so the RWAF (leading in rabbit welfare) recommend a minimum of a 6ft x 2ft base/sheltered area (Dog crate is a good idea), and a run/puppy pen of 8ft x 4ft. This is the minimum size for lock up time, permanently when you're out, and when you're in she can free range 24/7. If you address this issue she will be able to act normally and won't feel cooped up.
You can have a look at the housing sticky for ideas
http://forums.rabbitrehome.org.uk/showthread.php?304613-Indoor-Housing
Please ask if you've got anymore questions x