Q: Amplifier's Output filter not having the Correct Cut off frequency
You have two factors at play here. One is the output impedance of the amplifier, which seems to be of the order of 100-150 Ohms. This impedance gets added to the 560 Ohm load, which shifts the -3 dB point. The other factor is that you have two RC filters in series, one is 500k/1uF on input, and the other is 500R/1mF on output. Transfer function of these two sequential filters is a product of two RC functions, and phase also shifts, which again shifts the -3dB point into higher frequency area.