Yawning alters the conformation of the external auditory canal by displacing the mandible, which articulates with the tympanic plate of the temporal bone adjacent to the canal.

The seal might be so good that a small pressure differential happens as cabin pressure drops, which causes some issue with the microphone or speaker. Yawning might break that seal, or otherwise cause pressure equalization. Why only the left one? Apple might put some kind of special signal diagnostics or sensors in that side that bugs out under those conditions, or maybe human anatomy on the left side is consistently subtley different in a set of people.

Because this doesn't happen to everybody it could be some kind of "instrument effect" where the particular shape of someone's ear canal, and the interaction with their ear drum and the speakers and sensors in the app creates this tone, likely assisted by the constant driving signal of air cabin white noise.