Assuming you mean the frequency counter library at http://interface.khm.de/index.php/lab/experiments/arduino-frequency-counter-library/, it uses timers 1 and 2, and disables timer 0 during the gate time. This means that none of the PWM pins on a Uno will work while you are measuring a frequency.
If the frequency you want to measure is less than about 10kHz, there are other ways of measuring it that take over only one timer, or even no timers at all.