One of the common non-destructive testing (NDT) techniques for detecting surface cracks in metallic structures involves the use of microwave signals and an open-ended rectangular waveguide with a standard flange as the probing device. In this method, the presence of a surface defect is identified by observing variations in the detector voltage, which corresponds to the total electric field at a specific point inside the waveguide. To facilitate and accelerate the inspection process in practical applications, a finite air gap — referred to as the liftoff distance — is typically maintained between the waveguide aperture and the metal surface. This paper, through detailed and systematic simulations using ANSYS HFSS, demonstrates that at certain frequencies, even minor changes in the liftoff distance can lead to significant variations in detector voltage. These changes may be mistakenly interpreted as defect indications, potentially leading to false alarms and unnecessary inspections. To validate the simulation-based findings, experimental measurements were also performed using a Vector Network Analyzer, specifically the Keysight Technologies N9952A model. The paper presents a comprehensive study of optimal frequencies for a WR-90 waveguide with a standard square flange in the frequency range of 8 GHz to 12.5 GHz, focusing on minimizing sensitivity to liftoff distance variations. Simulation results show that when the liftoff distance varies between 0 mm and 0.5 mm, the detector voltage exhibits the lowest sensitivity at 8 GHz, 10.495 GHz, and 12.5 GHz. Furthermore, when the liftoff variation extends up to 1 mm, the optimal frequency slightly shifts from 10.495 GHz to 10.240 GHz. To further confirm the proposed optimal frequency, a measurement at 10.5 GHz was carried out using LabVolt microwave laboratory equipment from Festo Didactic. The experimental results show a good agreement with simulation predictions, supporting the validity of the selected frequency range for reliable surface crack detection with minimal liftoff sensitivity. In order to investigate the sensitivity of the proposed frequencies in crack detection, simulation results for two slots with different depths are presented and analyzed.