most if not all nanoVNAs only output a square wave signal due to the on-board clock chip (e.g., Si5351)
square waves contain the fundamental frequency plus odd harmonics (3rd, 5th, etc.), which means the VNA injects energy at multiple frequencies at once rather than a single, pure tone. This contaminates S-parameter and frequency response measurements, especially when characterizing narrowband or resonance circuits where harmonics may overlap with other system frequencies.
many RF devices, filters, and components are designed to respond only to a clean, single-frequency (sine) excitation. Square waves defeat this by exciting unwanted resonances, giving misleading results for insertion loss, reflection, and filter performance.
VNAs rely on precise calibration at known frequencies. Harmonics from a square wave interfere with measurement by creating multiple frequency responses simultaneously, making accurate calibration and measurements impractical for demanding applications.