Product Version: NetBeans IDE Dev (Build 201505020001)
Java: 1.8.0_45; Java HotSpot(TM) 64-Bit Server VM 25.45-b02
Runtime: Java(TM) SE Runtime Environment 1.8.0_45-b14
System: Windows 7 version 6.1 running on amd64; UTF-8; pl_PL (nb)

The following code leads to the "Confusing indentation" warning. I applied code format using the default formatting style.

Testcase:

    public void demo(int check, boolean a, boolean b) {
        switch (check) {
            case 1:
                if (a) {
                    if (b) {
                        System.out.println("a AND b");
                    } else {
                        System.out.println("a AND NOT b");
                    }
                } else // a is false
                if (b) {
                    System.out.println("NOT a AND b");
                } else {
                    System.out.println("NOT a AND NOT b");
                }
                break; // <-- warning
            case 2:
                System.out.println("Don't case");
                break;
            default:
                throw new IllegalArgumentException(check + " is not allowed");
        }
    }

Note the warning disappears after removing the "a is false" comment and reformatting code. The strange formatting and comment location comes from bug 252303.