Before starting your measurements with the Reference 4 Measure app, it is important to make sure that your microphone input isn't routed directly to the audio device outputs, bypassing the computer, or in other words, that the direct monitoring is not enabled on your audio interface.
What is direct monitoring?
Direct monitoring takes the input signal from the audio interface and sends it straight to the line and headphone outputs on the audio device. This is great for monitoring the input signal with near-zero latency. If you, however, wish to apply effects on your input signal via your DAW or calibrate your speakers using Reference 4 Measure software, you will need to use the normal 'input monitoring' (also called software or DAW monitoring).
Direct signal is not converted from analog to digital and is not processed by the computer which is essential for the Measure software to make calculations when correcting the frequency response of your speakers in your room. Since the processing of the signal via the computer will take more time it will be slightly delayed and when mixed with the direct signal this is what can cause phasing issues and/or feedback.
How to disable direct monitoring?
A lot of audio interfaces will have a button or a switch on the device to disable direct monitoring.
A rotary knob can sometimes also be used to dial in the amount of the software processed signal versus the direct signal. In that case, the knob needs to be set 100% to software monitoring (marked 'USB' in the image below) to be used with Measure software.
If an audio interface doesn't have a button or a knob on the device to control direct monitoring, it can also be controlled via app/control software. Usually just muting the input channel for the microphone will do the trick but there are some devices where this will also mute the software/DAW monitoring so alternatively, just moving the microphone input channel's fader down to infinity will disable the direct monitoring as well.