You need to check if the file clicked is the one loaded by the player. You can do that by wrapping the track-setting code and the player.load in this if-statement.
if ($('#player_track').attr('src') !== track){
$('#player_track').attr('src', track);
player.load();
}
The whole code:
window.player = document.getElementById('player');
$('ul.tracks li span.play').click(function(){
$('ul.tracks li span.play').find('i').removeClass().addClass('fi-play');
var trackid = $(this).attr('id');
var track;
if(trackid == 'play1'){
track = 'img/music.mp3';
} else if(trackid == 'play2'){
track = 'img/music2.mp3';
} else {
track = 'img/music3.mp3';
}
if ($('#player_track').attr('src') !== track){
$('#player_track').attr('src', track);
player.load();
}
if (player.paused) {
player.play();
$(this).html('<i class="fi-pause"></i>');
} else {
player.pause();
player.empty();
$(this).html('<i class="fi-play"></i>');
}
});