16 bit PWM doesn't go to absolute 0V
You've got two possibilities:


You can't have full off in "non-inverting PWM" mode
You can't have full on in "inverting PWM" mode


In the Arduino core it's solved by turning off the PWM output and setting logical 0 or 1 for corner values.

And if you need full off but you don't need full on, you can use inverted PWM mode.