Short answer: by doing your charging in the moon you are inadvertently practicing moon magic rituals.
Not long ago a buyer asked me why I recommend against charging your crystals in moonlight. In my first blog post on here, I mentioned that the moon is a negative energy source. We live in a duality universe. Therefore, where there is light there is dark, male and female, yin and yang, sun and moon. The list can go on. Everything that is, has a polar opposite. Night or dark is associated with the negative energy. Most of the advice that you come across about how to charge your crystals and what have you comes from Wiccans and magic practitioners. Here's the thing though, not everyone who likes crystals is a practicing witch and by no means do you have to be. Another thing is, it's all made up. Don't get me wrong, magic can do harm to people if the person practicing that magic has a direct DNA link to that person. Crystals aren't magical and they aren't extraterrestrial. The are terrestrial minerals of the earth. They are no more magical than a diamond.
Think about what often happens around a full moon. People behave out of character, they can tend to be more negatively emotionally charged. It's where the word lunatic originated. When the Moon is full it is exerting it's strongest gravitational force upon the Earth. We have the highest tides during this time. So being that it is at it's peak energetic strength when it is full, it is the least desirable time that you would want to put a stone that can hold energy out under it to absorb it's negative effects. So by taking that advice you are inadvertently practicing moon magic rituals. Are you seeking out crystals because you want to perform moon magic? Do you know what you are doing, and what you are truly exposing yourself to? I know of what I speak when I advise this to you.
Having a crystal collection can be very enjoyable. There are many different types of crystals being discovered all the time and they are just beautiful. They are amazing holders and conductors of energy. You can charge a crystal with the type of energy that would be most beneficial to yourself and your surroundings. You can even use a quartz crystal to boost the energy of another crystal. Therefore if you are seeking out a life with more positive experiences, positive state of mind and emotions than you want to draw and retain the positive energies from the universe to you, not the opposite. The Sun is creative and the Moon is destructive or chaotic.
Think about how your mood boosts when you are out in nature and have the warm sunlight casting down on you. It provides your body the necessary energy for the skin to produce it's own Vitamin D. Plant life grows in the sun. They need a certain amount of sun exposure to thrive, so logically you would have to conclude that the Moon does not generate life or positive energy. You want things around you that are going to support your growth and your intentions, not work against them.
Understanding astrological influences of the celestial bodies and their affects on us can be extremely helpful and you can learn when energies are present at given times of the month or calendar in general so that you can mitigate their negative influences on your chart, but you really don't want a repository of negative energy living in your home. Hope this helps clarify, and I will leave you with that.