You've been tripped up by the notorious "defining functions inside a loop" problem.
Use "forEach" instead:
tempgame.stats.forEach(function (stat) {
db.users.find({ username: stat.user }, function(err, res){
if( err != null){
//handle errors here.
} else {
var userstats = res[0].stats;
if( stat.score > userstats.bestscore ){ //this is where it chokes
userstats.bestscore = stat.score;
}
//code here to pass back new manipulated stats
}
});
});