private int penaltiesInSubBoard(int i, int j, int scope, int[] skips) {
		int penalties = 0;
		int[] set = new int[chromosomes.length()];
		for (int y = i; y < i + scope; y++) {
			for (int x = j; x < j + scope; x++) {

				int value = -1;
				if (board.get(y, x) == 0) {
					value = chromosomes.get(y).get(x - skips[y]).allele();
				} else {
					value = board.get(y, x);
					skips[y]++;
				}

				if (set[value - 1] >= 1) {
					penalties++;
				}
				set[value - 1]++;
			}
		}
		return penalties;
	}
Penalties are issues in rows, columns, and issues in sub-boards (3x3).
"Issues" mean repeated numbers.
jenetics.example/src/main/java/io/jenetics/example/sudoku/SudokuGrid.java