In order to calibrate your speakers the distance between them should be at least 50 cm (20 in). If the speakers are closer, try moving them apart and retake the measurements.
If your speakers are more than 50 cm (20 in) apart and you are still getting this error, please make sure that you have routed your outputs correctly. When you choose your output channels at the Hardware Setup stage in Measure app, please listen carefully to the test track and make sure that when the voice says 'left speaker' and 'right speaker' the sound is coming only from the left speaker and right speaker accordingly and there is no left signal bleeding into right, and vice versa.
If the problem persists, please contact support.