A guess would be that the wings flap at such a rate that the disturbances in the air are in the range of human hearing. Reading around, this seems to be a fairly common explanation, however other places say that this is actually false. They say it's actually the deformation of the fly's thorax that causes the noise.
Other sources mention the air passing through spiracles, "tiny airways used for respiration". Apparently bees "buzz by vibrating their wings and bodies and pushing air through spiracles", which is likely similar to flies. In conclusion I'm still not really sure what the exact correct answer is.
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