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";
}
}
Remark: I have implied the desired logic from Athanasius output rather than studying your code, so I hope I got it right...