In the Bujinkan this process becomes obvious the more you explore. Usually someone's training goes a little like this:
Shodan to Godan: More basics. But also serious study of the ryuha that make up the Bujinkan. A focus on weapons. And more advanced concepts of strategy as it connects with distancing, timing and angling. During this time, the student may begin to encounter contradictions and things that are inexplicable in the training. Some are discouraged by this. And some refocus on the many ryuha kata and weapon skill acquisition.
After Godan: Hatsumi Sensei says,
Once one passes the Godan test his training changes into mienai(見えない)-keiko (unseeen training) then into wakaranai (分からない)-keiko (incomprehensible training).
Many of us have felt these things from our teachers or from Soke. Hatsumi Sensei always states that he is not teaching technique but rather a feeling. The problem is, the closer you examine this training the more it dissolves into mystery. My own experience is that it cannot be taught. You have to teach it to yourself.
When I catch a feeling from Hatsumi Sensei, I hold it close in my heart. I use it like a sense memory, an affective or emotional memory. One that I can resonate with at the appropriate moment. Then I compare my results to my teachers. When it works, all I can do is smile when I see the puzzled look on my student's face.
This process is mysterious and wonderful.