Spontaneous Mutation Syndrome
Given that the genetic prototypes stored in Friend Computer's databanks are perfect reproductions of the human form, and that the genetic variances The Computer introduces to the genotypes prior to cloning an individual are well within any measure of reasonability, it seems obvious that the mutation that occurs to individual clones must occur after their decanting (which explains why only certain clones in an otherwise identical clone family express mutations, or why some members of the same clone family express different mutations). One way, perhaps the most common way, for these mutations to occur is through Spontaneous Mutation Syndrome (SMS).
The effects of SMS are varied, one might even say random. Typically, they involve the subject screaming loudly, clutching at anything in reach and begging quickly for his own termination. R&D spent a great deal of time research SMS. The division determined the connection between SMS and combinations of Bile Suppressant and dentifrices (such as Toothpasty_Supplement_#5 & 6) and other possible contributors. Unfortunately, during this investigation, the division suffered an outbreak of SMS themselves. In the ensuing confusion the scientists did not register their new mutations, and eventually, Vulture_Squadron_Bravo_9 was dispatched to terminate the lot of them. A group of registered mutants briefly continued the project, but having so many of them working together was deemed a security risk, the team was disbanded and the investigation closed.
There are many possible sources of SMS, known or suspected, including GeneScan_Images, certain exposure to power service providers (note the increased rate of SMS around Nuclear_Facility_RON-372/B), and possibly even the Thirty-second_Flavor. However, since SMS is so destructive to the very society of Alpha-Complex that we cannot even risk our R&D scientists to further investigate its final causes.
It's pretty clear that you're not R&D; they never know any limit on what they should be researching. But in this case I think you're wrong. The more destructive a thing is to Alpha Complex, the more important it is that we discover its causes so that we might root it out. I mean, by your logic, the infectious nature of Communism makes it too risky to assign Armed Forces squadrons to exterminate Commie_Mutant_Traitors, and I think we can all agree that that would be ludicrous.
No, I was in R&D only a brief while before the TON Subsector explosion. I finished this section very late in the daycycle, and perhaps will update the main entry accordingly. What I meant to say is that this is research is too important to trust to a group of mutants, even registered one. And yet, each wave of researches invariably turn out to express Spontaneus Mutation Syndrome and, in the end, must be terminated. I am sure you would agree that we can not afford to send Commie Mutant Traitors to erradicate the Commie Mutant threat, correct? It's really the same thing.
Then assign ResearchBots to study the problem. Bots don't mutate.