Well … admittedly, hatch defects can be quite gruesome, so it can be rough for a sensitive breeder, especially if (and no offense intended to the breeder in one of these asks) the available genetic pool is … less than ideal for viable offspring, to put it as lightly as possible.
To put it bluntly, meanwhile, the worst of these will result in death, either shortly after hatching or, well, long after. Such deformities can range from abdominal hernias (in which the abdominal wall isn’t fully developed, causing internal organs to press against the skin—which is a condition that is not at all viable for life) to conditions in which the charmander will refuse to eat (which is possible to reverse with a lot of hard work) or in which the charmander will build up fluids beneath its skin slowly and for reasons that aren’t entirely understood in the pokémon medical world (which is not possible to reverse and will also result in death months after birth). Some charmander may even develop open sores due to an underdeveloped scale and/or immune system, although this, too, can be treated. However, if your charmander is born without scales or with an inability to produce more, that may make life somewhat painful for it, and battling with such a charmander is not recommended. They simply can’t recover as quickly as charmander with healthy scales, and wounds are more likely to become infected.
However, there are plenty of other conditions that are perfectly viable for life. Sometimes, charmander may be born blind. They could be born missing limbs, claws, or toes. Some have kinked tails (although if a charmander has a kinked spine—that is to say, spinal issues further up the column—then that pokémon may struggle when battling, just as a forewarning) or flames that burn a little dimmer than most, even when the charmander is perfectly healthy. Some have significant underbites or overbites (which only require some minor assistance for feeding when the charmander is young—they will learn to feed themselves eventually), and some are born without eyelids (which require you to administer eyedrops when they’re young until their eyes adapt). Some are simply born too soon and either have their yolk sac attached (which will fall off without any issue on its own) or are otherwise smaller than the rest of the clutch. As you can tell by the abundance of notes throughout this paragraph, all of these conditions result in charmander that can absolutely lead long and healthy lives; it’s just that some of these will require care, especially early on. And before you ask, no, evolution doesn’t “resolve” any of these issues. A charmander born missing a limb will be missing that limb as a charmeleon and charizard, but rest assured that this is perfectly natural and that the pokémon in question is very likely still perfectly healthy.
As a note, all of these deformities are possible in both standard and shiny charmander. Shininess doesn’t really increase the chances of a charmander being born deformed, as many of these deformities depend on a variety of factors entirely unrelated to a charmander’s color, from temperature and humidity of the incubator to genetic mutations on separate parts of a charmander’s DNA from the code that controls pigmentation.
The Pokédex According to Bill 