Arduino Micro tone() PWM Pins according to the tone() documentation using tone() interferes with PWM output:


  Use of the tone() function will interfere with PWM output on pins 3 and 11 (on boards other than the Mega). 


On my Arduino Micro it seems to interfere with PWM on pin 5. After using tone() the PWM does not seem to work anymore. If I use pin 3,9 instead everything works fine.

So can someone explain why that is happening and if there is a way to circumvent that?
The pin 3 and 11 only refers to boards based on the ATMega328. On these boards timer2 is used by tone, disabling PWM on pins 3 and 11. See Majenko answer about timers.

The Micro (ATMega32u4) tone uses timer 3, which is connected to pin 5 only.

So on the Micro, just don't use pin 5 for PWM when using tone.

Secondly don't trust everything on the arduino.cc website. There quite a bit of misinformation on there.