List of words which violate gender rules

No gender rules are being violated in your examples, because there are no rules. Spanish has two genders, but that's not the whole story.

1. There are epicene nouns which have one form and one given gender, no matter what they refer to, even if they refer to a person or an animal with a known biological sex. An example: persona.
2. There are common nouns which have one form but can take either gender (which is marked by the article and adjectives, if at all), such as joven and pianista. In this case the gender indicates the biological sex.
3. There are ambiguous nouns (not many) which have a single form but can be either gender. In this case the gender means nothing (it doesn't indicate sex).

Those are the rules, if you will. If grammatical gender had to be correlated with biological sex, then Spanish would have to have a "neuter" or "inanimate" gender and most nouns in Spanish would belong to that gender. That might happen in some languages, but not in Spanish. (It did not happen in Latin, which did have three genders, and does not happen in German or Icelandic either, which also have feminine, masculine and neuter.)

There is no logical reason "why" gender or noun-class assignments are manifested the way they are in Spanish or any other language. Languages have their own internal rules which are not bound by what we think of as logical or rational. The internal logic of Spanish arbitrarily permits some elements to be variable by gender or sex, and not others. In the end, all language is arbitrary, except perhaps onomatopoeia.

The word "Joven" is an adjective, but the others words are nouns. Every noun has a gender but the adjective is the complement. When you write "el joven", actually said "el hombre joven" and "la joven" means "la mujer joven". About the nouns, in some dialects you could use "la bebé" and some people said "la personaje de la obra" (from recent times, 2 or 3 decades ago), but you should use the original gender