Q:

Why there are messed up teens in a world where everyone can be designed to be perfect

I have a book where in the future a sterility disease spreads across the world making people unable to have children. Then, a company rises to power and using CRISPR are able to make babies again. Later parents are able to design their children completely; eye color, hair color, body type all that.
Well also in this world is what are called "Freaks" teens who have had the wrong Gene's activated and so they grow up deformed. (My main character is super fat instead of muscular). Because the sterility disease that the world is still recovering from, it is illegal to kill The Freaks. Then someone, for nefarious purposes, starts killing The Freaks.
The company also is the only establishment to work for. so they hold like a lottery see who gets the good jobs out of the "poor". The winners of the lottery are then stuck in a competition to see who can make it and be employed. Those who lose are kicked out and left to die on the streets.
My dilemma

Why are freaks being made? I had the idea originally that genetics Is a finite science and human error causes mess ups. But a company of this size would only employ the BEST, and would catch on to the ones messing up. I could chalk it up to beginners mistakes but again that seems unlikely...
I had another idea that maybe the poorer people are having their kids make from a cheaper virus with CRISPR or a more diluted version of the virus that is more prone to mistake. But then again why would the company sell it in the first place if they now have to pay to kill off the people they made...

A:

CRISPR isn't perfect
Alright, let's get into the science behind CRISPR gene altering and why it can fail horribly. CRISPR is pretty awesome, it's a fairly accurate gene splicing technique which we borrowed from bacteria which lets us cuts out the parts of DNA we don't want. It's pretty accurate, given that we can give it direct parts of the DNA to cut. Unfortunately, that's the only thing it does. It's like when you want to assemble a ransom note so you use a pair of scissors to cut out sections of a newspaper. Except all CRISPR can do it cut out sections. If you want to take those snips, or more accurately what we're trying to do here, take the newspaper and replace the words you've cut out with other words that make sense, you need other mechanisms to do that. And we don't have those kinds of mechanism, we just kind of just release the DNA into the target zone. (Okay, it's a little more directed than that. But not like a lot more complicated. The method is nowhere near as good as CRISPR, which itself isn't perfect.)
Basically, CRISPR isn't 100% successful - which makes sense. This isn't a computer program that's being edited bit by bit - you're dealing with biological life which always has a chance of failure, and is subject to weird phenomena like Browning Motion. Even in the future, it's highly unlikely you'd be able to have a 100% success rate and what will most likely happen is that you'll make these 'designer babies' in large batches (maybe like 100 at a time, especially if you're doing multiple gene edits). Also, since we're in the future, we'll have mastered the whole 'artificial womb' thing, so everything which seems viable can just be tried, especially if children are needed. 
So, recap: CRISPR isn't perfect, a lot of designers babies get made, artificial wombs for all, and the Freaks are a result of that.

A:

Different offers
Making a perfect human is quite difficult, needs lots of quality control, paperwork, etc.  and therefore it's expensive. However, you can avail of the cheaper option. But this has none of the quality assurance that the "Platinum package" has, and therefore carries a much greater risk of deformities.
This way you don't have to worry about "The BEST" employees screwing up, it's just that the customer didn't pay enough for them to put in the meticulous attention to detail that's required.

A:

There is more to the sterility disease than just sterility.
Where does this disease come from?  How does it work?  Maybe people in your world still do not really understand (a la Children of Men).  The CRISPR thing was a workaround.  
The sterility disease does not roll over that easy.  Sterility is the main thing and if a fetus dies in utero that is the only manifestation.  But there are other aspects to this disease, and in some persons this disease can affect more than one system.  Bypassing the most lethal part with CRISPR allows babies to be born despite being infected, but secondary and tertiary effects of the disease can affect a subset of persons.  It is hard to anticipate all the possible effects of this disease and sometimes it can still affect an individual.  Thus the freaks.  

