Starting with the iPhone 5, Apple decided to move the noise-canceling microphone from the top of the iPhone, where it was located in earlier versions, to the back by the camera and flash. In environments with background noise, if this microphone is covered, it will cause your voice to sound muffled. However, this is easily fixed by leaving some space between the covers when you're talking on the phone. If the background noise can reach that microphone, the muffled sound should be eliminated.
Alternately, the noise-canceling microphone can be disabled by going to Settings > General > Accessibility > Phone Noise Cancelation. Switching this OFF will prevent any interference of the sound from that rear-facing Mic.
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