There are people who misunderstand meanings based on context. Somehow a word is simply misunderstood.
Take a very common example: prodigal. The word originally meant being bad with money, but thanks to its almost exclusive association with a particular parable in the Bible, people now understand it to mean run-away (still an adjective). The tale is now seen as a father accepting his son back after leaving, rather than a father forgiving his son for squandering his inheritance.
The same can be said of 'arcane.' As Tiredofgaggs said, it simply means 'hidden.' It's the same as 'occult' in many circumstances. Many magical traditions were exclusive for a long time, thanks to many factors (not really worth getting into here), and being exclusive, the people who practiced certain traditions wanted to keep it away from others (such as some forms of Hebrew mysticism practiced by the priests being kept secret from the rest of the Jewish population, and not to mention various 'secret societies' which became rather popular in Europe and some which still exist).
The knowledge of these practices is arcane knowledge, but people have associated the term 'arcane' with more, and specifically with things related to a magic practice. And since many of these traditions at least claim much older -- and still hidden -- roots, the term is also attributed to being ancient.
But really, so much previously hidden material -- at least introductory material -- is being published or otherwise made available, many things hidden are no longer such. But they are still considered arcane by nature, thanks in part to the ever-evolving etymology of words.