Say you have an audio clip of 40 random notes in the scale of C
lasting 90 seconds and middle C is played just 3 times in this clip.

The user clicks a button when they think they have head middle C. How
can you tell if they were right?!

Some how you need to know how long into the clip each of the middle
C's were and whether the user clicked at these times?

Play the audio clip in a sequencer. Arm a MIDI track for recording.
Make the button they press a MIDI controller of some sort.