We present a sensitivity analysis on TRL calibrated S-parameter measurements of membrane circuits in the WR-03 waveguide band (220-325 GHz). The impact of waveguide and membrane circuit misalignment, as well as waveguide dimension mismatch is investigated. The analysis is performed for the thru-reflect-line (TRL) calibration applied to E-plane split waveguide blocks carrying membrane circuits. The analysis shows a large influence of the waveguide width tolerance on transmission and reflection phase after the TRL calibration. For a 20 mm long rectangular waveguide with a ± 5 µm width tolerance a phase uncertainty as large as ± 45° for reflection and ± 30° for transmission measurements is observed.