Your algorithm is simply not correct. First you need to compute the average and then other number. The statistical variance is the sum of the squares of the deltas of your scores from the average (and would give you one value for the complete series). Your variance seems to be the difference between each score and the average. Does that work:
public static void deviation(double[] scores, double[] variance)
{
double sum = 0;
for (int i = 0; i < scores.length; i++){
sum = sum + scores[i];
}
double average = sum / scores.length;
for (int i = 0; i < scores.length; i++){
variance[i] = scores[i] - average;
}
}