Bad grounding / routing / layout / filtering? Absolutely possible...
You didn't indicate if you made any measurements or observations (or what "clicking" is), but I'd be willing to guess the controller is in a low power (bang-bang) regulation mode, and this is causing modulation which is picked up by the amplifier. Normally, a controller has a buzzing or whining sound when in this mode, but perhaps it's doing it slow enough that it sounds like a "click". The amplifier, in turn, is disturbed by RF energy coupled in by poor layout or something like that. The amplifier itself should be very well filtered and grounded, because it is producing RF as well, which needs to be contained as well as possible to keep offset and distortion low, prevent oscillation, and radiated emissions.
Tim