Program: 108166
Project: 108166
Buggy source:
/** 
 * Returns the master function including the object function and the derivative functions
 * @return
 */
private Function<Vector2D,Pair<Vector2D,SquareMatrix2D>> getFunctionsIterative(final int[] classes,final double u,final double n){
  return new Function<Vector2D,Pair<Vector2D,SquareMatrix2D>>(){
    public Pair<Vector2D,SquareMatrix2D> evaluate(    Vector2D input){
      Vector2D object=new Vector2D();
      SquareMatrix2D derivatives=new SquareMatrix2D();
      double t=input.x;
      double a=input.y;
      double d1=0;
      double d2=0;
      double d3=0;
      double d4=0;
      double d5=0;
      double o1=0;
      double o2=0;
      double o3=0;
      double o4=0;
      for (int i=1; i < u; i++) {
        double val0=(t + (i * a));
        double val1=1d / val0;
        double val2=i * val1;
        double val3=1d / (val0 * val0);
        double val4=i * val3;
        double val5=i * val4;
        d1+=val3;
        d5+=val4;
        d3+=val5;
        o1+=val1;
        o3+=val2;
      }
      checkInterrupt();
      for (int i=0; i < classes.length; i+=2) {
        int key=classes[i];
        int value=classes[i + 1];
        double val0=t + key;
        d2+=1d / (val0 * val0);
        if (key != 1) {
          double val1=0;
          double val2=0;
          for (int j=1; j < key; j++) {
            double val3=j - a;
            val1+=1d / (val3 * val3);
            val2+=1d / val3;
          }
          d4+=value * val1;
          o4+=value * val2;
        }
        checkInterrupt();
      }
      checkInterrupt();
      for (int i=1; i < n; i++) {
        o2+=1d / (t + i);
      }
      object.x=o1 - o2;
      object.y=o3 - o4;
      derivatives.x1=d2 - d1;
      derivatives.x2=0 - d5;
      derivatives.y1=0 - d5;
      derivatives.y2=0 - d3 - d4;
      return new Pair<Vector2D,SquareMatrix2D>(object,derivatives);
    }
  }
;
}

Fixed version (ground truth):
/** 
 * Returns the master function including the object function and the derivative functions
 * @return
 */
private Function<Vector2D,Pair<Vector2D,SquareMatrix2D>> getFunctionsIterative(final int[] classes,final double u,final double n){
  return new Function<Vector2D,Pair<Vector2D,SquareMatrix2D>>(){
    public Pair<Vector2D,SquareMatrix2D> evaluate(    Vector2D input){
      Vector2D object=new Vector2D();
      SquareMatrix2D derivatives=new SquareMatrix2D();
      double t=input.x;
      double a=input.y;
      double d1=0;
      double d2=0;
      double d3=0;
      double d4=0;
      double d5=0;
      double o1=0;
      double o2=0;
      double o3=0;
      double o4=0;
      for (int i=1; i < u; i++) {
        double val0=(t + (i * a));
        double val1=1d / val0;
        double val2=i * val1;
        double val3=1d / (val0 * val0);
        double val4=i * val3;
        double val5=i * val4;
        d1+=val3;
        d5+=val4;
        d3+=val5;
        o1+=val1;
        o3+=val2;
      }
      checkInterrupt();
      for (int i=0; i < classes.length; i+=2) {
        int key=classes[i];
        int value=classes[i + 1];
        if (key != 1) {
          double val1=0;
          double val2=0;
          for (int j=1; j < key; j++) {
            double val3=j - a;
            val1+=1d / (val3 * val3);
            val2+=1d / val3;
          }
          d4+=value * val1;
          o4+=value * val2;
        }
        checkInterrupt();
      }
      checkInterrupt();
      for (int i=1; i < n; i++) {
        double val0=(t + i);
        d2+=1d / (val0 * val0);
        o2+=1d / val0;
      }
      object.x=o1 - o2;
      object.y=o3 - o4;
      derivatives.x1=d2 - d1;
      derivatives.x2=0d - d5;
      derivatives.y1=0d - d5;
      derivatives.y2=0d - d3 - d4;
      return new Pair<Vector2D,SquareMatrix2D>(object,derivatives);
    }
  }
;
}