I think one of the causes is that some people struggle for years with music and then one day they learn a bit of theory and they experience a moment of enlightenment. Suddenly, all of their confusion is dispelled and what was once difficult is clear as day. They then think "if I had only know this years ago I wouldn't have struggled!". But they are wrong. It was the years of struggle that helped them understand the theory, not the other way around.
It's the "wax on, wax off" of Karate Kid and the wise old Mr. Miyagi.
I read a music theory book from the 1800s and in the first chapter the author stated that while he endeavored to write useful theory to help students they must realize that if some composition they write follows all of his rules but sounds bad, it is bad. And if they write a composition that breaks his rules but it sounds good then it is good. These are old, old ideas that we re-learn over and over.