So I started the regimen a little over a month ago mainly to clear up my back, but to get rid of the little bit of acne on my face as well. Everything has been working great. My back has been getting progressively clearer and my face has stayed clean. I've been impressed with all the products I've bought, and as a result of my great results, I've bought all of them. Starter kit, AHA, Body buddy, and most recently, Jojoba oil. This is where I've become worried though.
The night after using the Jojoba both my back and face broke out pretty bad. It's like I just undid all the work I had been putting in for the past month. I even was sure to use a small amount of the oil as to not overdo it.
Not only this, but I've had some strange sideffects. I've gained large dark circles under my eyes as if I wasn't sleeping. And on of of my eyes, it looks like a bruise. Kind of like a black eye.. Nothing happened to my eyes. I just started using the Jojoba.. What's going on here? Everyone seems to love the Jojoba oil, but something about it isn't working with me..
sounds like an allergic reaction. I'm not allergic to much, but there is an eye cream I bought once that made my eyelids itch like crazy and puff up a little. Since jojoba oil is supposedly non-comdomgenic ( or whatever that crazy word is) I don't think it's an actual break out you're getting, but rather, hives. You should stop using it. There are other things you can try to alleviate severe dryness due to the BP. I think I've heard that coconut oil isn't supposed to break you out.
I've been using Jojoba oil by itself for awhile now because I didn't have any moisturizer, but I just purchased Cetaphil and found it mixes well, but doesn't really need it, so I'm off Jojoba.
But I've found Jojoba oil gives me a healthy glow, so I don't quite understand this...
Are you positive the marks on your face are acne? They look like all the other pimples you've had in your life?
If you had an allergic reaction or your skin is very sensitive, I think if you cake on enough of any type of oil you may be able to clog up your pores with it, but I'm no expert. I've used it with success so I'm confused. 
That's strange because acne takes two weeks to form so you could not break out the day after right? Not to mention all of the weird side affects. I agree with Misselissa, you are probably allergic. You could try test spotting it and see if you get hives and bruises in that place.
I've used certain products that have broken me out the very next day. Sometimes if it's an extreme irritation, your inflammation process will start up: IE: acne.
How much jojoba oil are you using? You should only be using a couple of drops in your lotion to start. You could also just be purging. A lot of people who start using jojoba oil complain of breakouts the first week or two of using it. That's something to keep in mind too. As far as the dark circles..that's really odd. The first thing that popped into my mind when you said that was that maybe the new "shine" your face has (IE: the jojoba oil leaving a slight sheen to your face) is giving you the impression of dark circles? Like shadows in a way, ya know?
Besides all that, you're your own best judge. If you feel like you're not benefiting from a certain product, than stop using it. However, if you feel like it'll just take time than keep using it.
Then again, you posted this about 2 weeks ago, so you've probably either already stopped using jojoba or your breakout subsided and you're still using it.
Technically, oral and topical antibacterial medicines can also can an increase in acne for the first couple weeks. Something to do with the immune system going into hyper-defensive mode; I don't fully understand it. But, it is different from purging. Usually it's a sudden wave of small pimples that subsides very quickly.