In what application are you having the microphone problems?
You may have to manually reset the audio daemon. To do this,
(1) Type in the search bar "Terminal" and click the Terminal utility.
(2) Type in "sudo killall coreaudiod" into the Terminal black box.
(3) It'll automatically show a warning sign and tell you to enter your computers password.
(4) Type in your Mac's password.
(5) Restart the application by exiting out and launching it again.
Let me know if that works?