Your,

    @arr1=sort($_[0]);
    @arr2=sort($_[1]);
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puts exactly one element in each array, a reference to the corresponding array. They will never match unless you compare an array to itself.

You want,

    my @arr1 = sort @{$_[0]};
    my @arr2 = sort @{$_[1]};
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Your for loop is more perlishly written,

    for (0 .. $#arr1) {
        if ($arr2[$_] ne $arr1[$_]) {
            print "Anchor/indicator mismatch in $arr1[$_]\n";
        }
    }
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but what you have will work fine.

You might be interested in the Algorithm::Diff package.