GaN field-effect transistors (FET) have low conduction and switching losses in high-frequency (>MHz) resonant wireless power transfer systems. Nevertheless, such systems impose a unique stress on GaN FETs owing to their non-ideal voltage waveforms. In this work, we report the observed non-ideal behavior in a 6.78 MHz magnetic resonant wireless transfer system that employs class-D GaN power amplifiers. The non-ideal waveform phenomenon existing at the output of the power amplifier is explained. The study analyzes the causes of this phenomenon, including the coupling coefficient k of the coil, the DC input voltage of the amplifier, and the load on the receiver. Each parameter is simulated and analyzed using LTspice. The influence of the phenomenon on the on-state resistance of the GaN device is proved in an experimental measurement, and the cause of the phenomenon is explained.The study combines a theoretical simulation and an experimental test to discuss the effect of this phenomenon on GaN power devices and proposes the corresponding solutions, which include the limitation of voltage, current, and power of the system, thermal management, and other protection measures.