Possible causes for sore ear when using audio amplifier (PAM8302A) and speaker at a reasonable volume
If it bothers your ears, definitely spend some time to investigate the cause. It's possible there is an ultrasonic tone or noise being generated. This could be from acoustic feedback (speaker to air to microphone), an electronic feedback path within your breadboard circuitry, or other source of noise (power supply switching, etc). Your need to insert a low-pass filter to reduce obvious feedback makes it even more likely you have a high-frequency feedback problem.
High-intensity ultrasound is known to damage hearing. At lower intensities it could cause auditory fatigue, and longer-term could cause hearing damage as well.
Get that oscilloscope connected to the amplifier output and see what's there. Don't count on a smartphone app spectrum analyzer or sound intensity meter -- the smartphone microphone and circuitry have an upper cutoff that may be below the frequency of your problem sound.