This is probably the only downside to a true hardwired bypass circuit! The input and output circuits of a pedal are coupled using a capacitor to isolate the signal from the DC voltages present on the internal circuitry. These capacitors often "leak" a tiny -- almost insignificant -- amount of DC current. When you disconnect one end of the capacitor, it tends to "float" toward the DC voltage found at the other end. When you stomp the button to turn on the effect, that floating end is suddenly connected to a zero voltage, and the capacitor has to suddenly replace the charge lost during the "float" time. This, of course, sounds like a pop or a click. This isn't an issue easy to address; its something all true bypass pedal suffer from. Most guitar players just live with it. However, the easiest way of bypassing the problem is either to turn the pedal on and off more frequently than you really need as that will prevent the DC from building up. It the case of a PolyTune pedal, you could get a volume pedal with a tuner out or use another device to split your signal and connect PolyTune to that. This way you could just have the PolyTune on all the time and not worry about it effecting the signal path (no more pops). FYI, many players keep a tuner active at all times to use as a reference or training tool for slide work, bends and tremolo arm work. Many of our pedals have the option of being switched to a buffered bypass circuit. Using the buffered circuit eliminates the true bypass pop and also helps prevent signal loss associated with plugging through multiple devices or using long cable runs. Another benefit to using buffered with your TC reverb or delay is it activates the spill over feature. Spill over allows your effect to ring out after you have disengaged the switch. Using this eliminates abrupt cut offs in effects allowing for a more artistic expression. Please consult your pedal's owner's manual
to see if it has a buffered option.