counts seen in serial monitor are approximately 70...... much higher than 50. I think I have to look at the waveform on the oscilloscope to check that first.
I don't confirm what you are seeing. I changed the millis() timer to micros() and set the measurement period = 1000. With tone(11,50000) I am seeing counts of 49 or 50 with a period from 1000 to 1012 us.
For more precise high speed counting, you want to have the period defined by a hardware timer an not a software one using millis() or micros(). See Nick Gammon's Frequency Timer sketch at Gammon Forum : Electronics : Microprocessors : Timers and counters