Don
Again, you are asking good, reasonable questions.
Mutations are not by definition a negative thing. Some are good, some are bad, and many are neutral. Of course, in real life there are shades of all three categories and it may be hard to classify a particular mutation. In the case of the mutation that prevents primates from making vitamin C, the word corrupted is a good word because one of the essential enzymes can no longer be produced because of a copying error. But it would be hard to classify this as much other than neutral because primates generally get adequate vitamin C from their diets.
In saying that it was corrupted, we are saying that something that was working before is no longer working. That is not to say that it was perfect. There are plenty of examples of things in living systems that work but that are not exactly optimized.
You ask So what/where is the evidence that it's not supposed to be the way it is? The main evidence is the simple fact that this is an ability that essentially all animals have. But for primates, this elaborate set of chemical machinery has been broken in one little spot. They have all the little parts needed but one of the parts has a very slight problem. But that problem is enough to disable the whole system. If they were designed perfectly to begin with, why do they have this useless set of machinery? It is key that all of the animals grouped together because of their morphology as primates are later found to share the exact same genetic characteristic. It is a small but important piece of evidence that all primates are related through a common ancestor.
It is when you start comparing more and more pieces of genetic information with morphology that the real importance begins to become apparent. That is why I put in the part about other mutations in my last post. By itself, the vitamin C thing could just be an amazing coincidence that the dozens or hundreds of primate "kinds" all developed the same mutation right down to the exact nucleotide. Long odds, but someone would make the argument just the same. (Math. For two animals the odds would be 1 / 230 = 0.0043. For 5 animals the odds would be 1 / (230*230*230*230) = 0.00000000036 or 1 in 2,798,410,000. Even for just 10 animals it is 1 chance in 180,11,52,661,463,000,000,000. Now think of the math for dozens or hundreds of times for the same mutation to be repeated in all the different primate "kinds.")
But then you start putting the other genetic data on top of just this one piece. I have already given you the example of how some genes can mutate and still remain effective. Looking at how much these genes vary from one animal to another can tell you something about how closely the animals are related. Looking at several is even better. Another example I neglected before for simplicity is what are known as psuedogenes. Let me give you an example of how you might get a psuedogene. One type of mutation is when two copies of a gene instead of one are made during the copying process. Now the genome has two copies of the same gene. One can continue to produce the needed protein even if the other mutates. The mutated, non-functioning gene is called a pseudogene. (I am not a biologist, so forgive me if the exact details are off a bit, the general idea is here.) You can also look at these pseudogenes the same way we have discussed above to check for relationships. Sticking with humans, we again find pseudogenes that we only share with other apes or other primates. The same animals that we share our morphological or physical, characterastics with. The little pieces of evidence just pile up until the string of coincidences necessary to explain them becomes rediculous without using common descent. That is if you do not think that even in the one case of the vitamin C sythesis that the odds became comical after a bit of the possibility of the same mutation happening that many times in so many different "kinds" and the mutations being passed on and becoming part of the gene pool of all members of that "kind" and that the mutation did not strike any "kind" outside of the primates. And time after time, the genetic data agrees with the morphology data.
As a side not, the duplication type of mutation is very important to evolution. Once you have the two copies of a gene, one copy can mutate without effecting the capabilities of the organism because there is still a good copy of the gene. The other gene may then mutate into something that does the original job better and replaces the old gene. Or it can develope a whole new function that helps the organism survive. When you look at the details of how systems in cells work, you often find new machinery evolving from a related bit of machinery that continues to do its same job while the new bit does something new. It is a great way to evolve those "irreducibly complex" systems that some like to say cannot evolve.
I hope I have helped somehow. I am trying to stay general and not go into to many details. I think that would just confuse you. It essentially boils down to saying that common descent explains much of what we observe. It is up to YECs to show that it does not, if they disagree, and how instantaneous creation of the various "kinds" better reflects the data we have.