There are two microphones in the Fairphone 2 (as in most other phones these days). Roughly speaking*, one is used during calls, and the other is used during conference calls and for recording audio on videos. There may be a hardware defect in your bottom module - this would only affect one of the microphones. Checkup may help diagnose this, or see below for manual instructions.
(*for noise cancelling the secondary microphone is used in parallel with the primary microphone)
More info:
https://fairphone.zendesk.com/hc/en-us/articles/213161166-My-microphone-does-not-work-properly