private int penaltiesInRows() {
		int penalties = 0;
		final int[] set = new int[Board.SIZE];
		int[] skips = new int[Board.SIZE];
		for (int i = 0; i < Board.SIZE; i++) {
			Arrays.fill(set, 0);
			for (int j = 0; j < Board.SIZE; j++) {
				int value = -1;
				if (board.get(i, j) == 0) {
					value = chromosomes.get(i).get(j - skips[i]).allele();
				} else {
					value = board.get(i, j);
					skips[i]++;
				}
				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