In cases like this I prefer to first classify each label by setting a flag in which array it is present. I do this by using bits (1 for @input_array, 2 for @input_A, 4 for @input_B). In the second step the labels are processed based on their flags.

use strict;
use warnings;

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 %flags;
$flags{$_} |= 1 for @input_array;
$flags{$_} |= 2 for @input_A;
$flags{$_} |= 4 for @input_B;

my %primaryCCO;
for (keys %flags) {
    next unless $flags{$_} & 1;
    print "$_: only 1 input is PI\n" if $flags{$_} == 3;
    print "$_: this is a wire\n" if $flags{$_} == 5;
    if( $flags{$_} == 7 ) {
        $primaryCCO{$_} = [1,1];
        print "$_: CCO = ( @{$primaryCCO{$_}} )\n";
    }
}
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Remark: I have implied the desired logic from Athanasius output rather than studying your code, so I hope I got it right...