That's actually an interesting possibility, if I understand you right. The basis behind the morphing technology is that it takes DNA to build a blueprint of a body, right? Theoretically, this would require copying the DNA over and over and over again, and each time DNA gets copied there is a possibility for mistakes which could cause mutations. Now, the Andalites probably thought of that, and so they may have created safeguards against copying mistakes while morphing.
However . . . DNA is also copied within every new cell of an organism. When an animal grows from an embryo into an adult animal, its cells split thousands upon thousands of times, and each split is an opportunity for mutations. This doesn't typically cause any problems for the animal itself, because DNA mainly just codes for proteins (and it's the proteins that determine how the animal grows and functions). And so as long as the animal has some cells that are making the right proteins everything tends to work out (except when some cells turn cancerous, but that's a different scenario entirely). BUT, when someone acquires DNA from an animal, they're only sampling a few cells. Those cells are probably going to have mutations compared to the animal as a whole. Mostly, they're probably not going to be serious mutations, but every now and then they could be.
Hmm, I wonder if that's what really causes morph allergies like in book #12? You just happen to acquire some 'bad' DNA that is so badly mutated that it would eventually kill you if you morphed it too often, and so the morphing technology rejects it.
