Probably due to magnetic interference from the wireless charger (it puts out a magnetic field that transfers power to a coil inside the back of the phone). See this Phone Arena article that explains how the S-Pen works and why magnetic fields can affect it:
Double pressure: how the S Pen stylus of the Note 4 works
Excerpt:
"First off, the S Pen doesn't have a battery, or another internal power source. Its circuit board gets incited by the electromagnetic field of the Note 4's dedicated display layer, for which you can find proof by hovering the tip of the S Pen over the display. This mode, called Air View, allows you to highlight links and preview stuff without even touching the display with the stylus - the distance from which Air View is possible, is the distance where the magnetic field of the screen kicks in to power the S Pen. The electromagnetic field is created by tiny coils and a control board, sitting behind the Note 4's screen, pushing power in the ether. The board excites particular coils by rapidly turning them on and off, creating the electromagnetic energy effect in the respective area. The power then gets transferred to the S Pen's internal resonant circuitry, and bounces back to the control board, this time carrying info such as coordinates, precise angle, and pressure applied."
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