It's because we're dealing with genetic mutations and combined genetics.
- Sometimes some mutations are more prone to defects than others. (Example: All spiders have neurological issues that make their head wobble to various degrees)
- Sometimes mutations do weird stuff when combined with others.(Example: Cinnamon and Black Pastels are generally fine on their own. But when combined into a 'super', they tend to be prone to spinal kinks and facial defects, such as duck billing.
- Sometimes mutations are not compatible with each other. (Example: Some mutations are lethal when combined and do not survive like the Super Champagne)
Some of these mutations/combinations would have otherwise been most likely selected out of the gene pool in nature. But in captivity they survive since there is no natural selection.
Here's a good reference to all the genetic issues in morphs:
http://www.owalreptiles.com/issues.php