From what I see you just try to see if they are equal, if this is true, just go with something like this:

boolean areEqual = Arrays.equals(arr1, arr2);

This is the standard way of doing it.

Please note that the arrays must be also sorted to be considered equal, from the JavaDoc:

Two arrays are considered equal if both arrays contain the same number of elements, and all corresponding pairs of elements in the two arrays are equal. In other words, two arrays are equal if they contain the same elements in the same order.

Sorry for missing that.

First things first, you need to loop to < a.length rather than a.length - 1. As this is strictly less than you need to include the upper bound.

So, to check all pairs of elements you can do:

for (int i = 0; i < a.length; i++) {
    for (int k = 0; k < a.length; k++) {
        if (a[i] != a[k]) {
            //do stuff
        }
    }
}

But this will compare, for example a[2] to a[3] and then a[3] to a[2]. Given that you are checking != this seems wasteful.

A better approach would be to compare each element i to the rest of the array:

for (int i = 0; i < a.length; i++) {
    for (int k = i + 1; k < a.length; k++) {
        if (a[i] != a[k]) {
            //do stuff
        }
    }
}

So if you have the indices [1...5] the comparison would go

1. 1 -> 2
2. 1 -> 3
3. 1 -> 4
4. 1 -> 5
5. 2 -> 3
6. 2 -> 4
7. 2 -> 5
8. 3 -> 4
9. 3 -> 5
10. 4 -> 5

So you see pairs aren't repeated. Think of a circle of people all needing to shake hands with each other.