Noise becomes more noticeable when you press the shutter button halfway down while using a narrow aperture in the A mode with [Anti-flicker Shoot.] set to On.
 Before pressing the shutter button halfway down
 When pressing the shutter button halfway down
This phenomenon occurs because the frame rate of the live view becomes faster in order to detect flicker. The shutter speed of the live view also becomes faster in accordance with the frame rate, and the amount of light decreases. The noise increases to compensate for the lack of luminance.
This noise does not affect the actual recorded image. However, if you are distracted by it, turn off [Anti-flicker Shoot.].