When you switch to speaker mode, the phone uses a different microphone than it uses during regular calls (it uses the one that is also used for recording audio when making videos). The bottom module, which houses the regular microphone, may either have (partially) lost connection to the rest of the phone or it could be a defect. The former can often be solved by removing the module and putting it back again, in the latter case you’ll need to contact Fairphone support to get them to fix it. There’s more discussion about microphones that don’t work here.
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