Hello ameezys, and a belated welcome to the Monastery!

You are using grep incorrectly. The block is applied to each element of the array in turn, setting $_ to that element. So

grep { @input_B eq $_ } @input_array
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is testing each element of @input_array against @input_B, which makes no sense. You need something along these lines:

for my $inputKey (@input_array)
{
    if (grep { $inputKey eq $_ } @input_A) ...
}
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As Marshall says, your requirements are not clear. I’m guessing you want to add an element to the hash %primaryCC0 when, and only when, that element is common to all three input arrays. In which case, the any function in List::Util is more efficient than grep:

use strict;
use warnings;
use List::Util qw( any );

my @input_array = qw( N1 N2 N3  N6  N7      );
my @input_A     = qw( N1 N3 N11 N11 N10 N16 );
my @input_B     = qw( N3 N6 N2  N7  N16 N19 );
my %primaryCC0;

for my $inputKey (@input_array)
{
    if (any { $_ eq $inputKey } @input_A)
    {
        if (any { $_ eq $inputKey } @input_B)
        {
            @{ $primaryCC0{$inputKey} } = (1, 1);
        }
        else
        {
            print "$inputKey: only 1 input is PI\n";
        }
    }
    else
    {
        print "$inputKey: this is a wire\n";
    }
}

for my $key (sort keys %primaryCC0)
{
    my ($CC0, $CC1)  = @{ $primaryCC0{$key} };
    print "CC0[$key] = $CC0\n";
    print "CC1[$key] = $CC1\n";
}
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Output:

16:27 >perl 1992_SoPW.pl
N1: only 1 input is PI
N2: this is a wire
N6: this is a wire
N7: this is a wire
CC0[N3] = 1
CC1[N3] = 1

16:27 >
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Note that although @{ $primaryCC0{$inputKey} } = (1, 1); works (because of Perl’s autovivification), I would prefer to use:

$primaryCC0{$inputKey} = [1, 1];
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which makes the creation of an anonymous array explicit.

Hope that helps,