Atari, repeating sounds
The action of popping a finger or a thumb off and onto an open or closed hole is called atari. It is used in shakuhachi playing to repeat a note when the score calls for a repeat and it introduces a split second of a higher or lower pitch into the air-stream. The physics of the flute are such that only the slightest movement of the finger off/on the hole is needed to create the desired effect. This often means the finger barely breaks its fleshy seal with the hole. If the movement is too overt, then the flute may be jolted and your embouchure discombobulated. If the movement is too slow, the modulation becomes a note triad.
There are some players who attack the hole on atari repeats, thus producing a 'pop' sound from the hole itself. This can be a musical ornament, but it should be used judiciously, otherwise a piece of music can get to sound like a video game.
Fingering
When holes are not being covered, unused fingers should be well away from the holes. There are exceptions though: for instance, trills may need the trilling finger to stay close to the hole.