What you've asked is a very general question... I'll try to provide a generalised answer.
Most of the illnesses/injuries that befall chameleons - especially the ones reported on these forums - are caused by improper husbandry, and would probably not be encountered by chameleons in the wild:
- MBD (and all its related complications): this is generally caused by inadequate exposure to UV light, improper supplementation, improper diet.
- URI: often caused by enclosures that are kept too wet, where bacteria can grow quite comfortably.
- Gout: due to improper diet and improper supplemention (usually too much supplementation or protein in the diet), possibly also due to inadequate temps for digestion.
- Conjunctivitis: cases have been reported recently of chams suffering eye problems and keeping their eyes closed due to using the compact (coiled) UVB bulbs.
- Heat burns: caused by placing heat lamps incorrectly, where chams can expose themselves to dangerously high temps and get burnt.
- Dehydration (and its resulting complications): although this could occur in the wild in cases of severe drought, I'm sure you'd agree that if a captive cham got dehydrated, it is probably the fault of the owner.
- Parasite infestations: chams in the wild often pick up parasites. In fact most WC chams come in with parasites. But if a CB cham that starts off clean of parasites eventually is infested by parasites, or contracts a bacterial infection, then it is usually due to unsanitary conditions in the cage or possibly through feeding infected WC feeder insects to the cham. If the parasite infestation gets bad enough that it causes serious health problems to the cham, then that is also owner negligence - fecal tests should be done regularly to pick up the presence of any possible parasites.
- Bacterial infections (other than URI): often caused by unsanitary conditions in the cage.
There are other injuries that befall chams that are not strictly the owner's fault, but can often be prevented by improved husbandry:
- Lost toenails: this is often caused by chams walking on fine metal screen. This can generally be avoided by using larger, PVC coated mesh, or fibreglass screen.
- Impaction/digestion problems: loose, uncovered soil/small rocks/bark or other substrates should not be kept in the cage where a cham can ingest them and possibly suffer an impaction. Also, only feeder insects of the appropriate size should be fed to chams. Too large insects can cause choking and impaction.
There are cases where chams are simply born with poor genetics or poor chances of survival. Females often lay large clutches of eggs, and not all the eggs are equally supplied with nutrients. Some of them don't form properly. Sometimes things go wrong with certain eggs during the incubation process. If these embryos make it through all these setbacks, they may hatch as chams born with inherent problems and slim chances of survival.
But these are the exceptions, rather than the norm when it comes to most of the health problems posted on these forums.
That's why it's so vital to study up and understand the husbandry requirements for chams before obtaining any. Even a perfectly born, genetically healthy cham doesn't stand a chance if the set up and husbandry practices are incorrect.
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