Is she spayed? If she isn’t, they aren’t actually bonded. You’ll need to separate them until 1-2 months post spay and prebond during that time. His behavior seems pretty characteristic of a hormonal male, which would happen if the female wasn’t spayed.

The female definitely needs to be spayed, and they should be separated now before you have more problems. This behavior that has started can lead to fighting and severe injuries. As has been stated, you can start the regular bonding procedures after several weeks have passed since her spay surgery.

Here are two good articles on bonding:

https://binkybunny.com/BUNNYINFO/tabid/53/CategoryID/9/PID/940/Default.aspx

http://rabbit.org/faq-bonding-multiple-rabbits/

But, here’s this weeks’ situation. She has started to honk/”growl” at him just getting near her, even when he has no intention of humping her. She seems highly on edge for some reason lately. Just now he started chasing her twice around the cage, then she jumped to the litter box and put her butt up against the wall again, thats when he just gave up, but she still kept honking even with him already gone. I went to pet her, and she even honked a little bit at my touch, so I stopped and just gave her some space. She then happily jumped back to him and lied down next to him where he was now relaxing.
I really don’t know what her behavior means lately, why is she so on edge? I’m sorry if this was a mess, I never write on forums and english isn’t my first language either. I’d love to get some insight on this.

Your English is fantastic!

It is highly likely she is experiencing what is known as a “false” or “phantom” pregnancy. Rabbits are induced ovulators, meaning ovulate after being mounted. With a false pregnancy, the rabbit goes through some hormonal changes and even has increased supply of blood to the uterus. They really believe they are expecting and often owners will see the rabbit build a nest and pull fur toward the end of these episodes. Desexing prevent female rabbits from having these episodes and it also cuts out the risk of them developing uterine tumours or other uterine infections. The risk is very high for intact female rabbits. 

 Hormonal fluctuations cause the rabbit tremendous stress and can lead to aggressiveness, growling and biting the days preceding the nest building. Pseudopregnancies can become chronic when a female remains intact, increasing the risk of developing reproductive disorders such as pyometra, hydrometra, or uterine adenocarcinoma, and/or mastitis.http://www.medirabbit.com/EN/Uro_gen_diseases/Pseu_preg/pseudo_en.htm

Your rabbits honking and being on edge very much reminds me of a rabbit I had that was actually pregnant. I only had her a week before she gave birth, but afterward, she was not vocal or really terrified at all. It was completely related to the pregnancy.

Did you have the boy neutered or did the previous owner have that done?
Are you absolutely sure he has been neutered or is even a male? (female rabbits do hump each other, especially when both are intact).

If the rabbits are not badly fighting but she is getting upset by him, I think giving her something where she can go to get away from him when she likes. A small hidey box they both cannot fit in or a shelf she can jump onto where only one rabbit will fit.

Ideally, it would be better to have her desexed for her health but also so they can live together more peaceably.

Even if your male bunny is fixed, only his testicles were removed. Not his penis. Female bunnies, if they fear unwanted sexual advances, have the ability to castrate the male bunny with their back claws. For the safety of BOTH of your bunnies- PLEASE separate them till you can afford to spay the female. She is still emitting hormones that can cause even a neutered male to become sexually aroused and exhibit breeding behaviors.