One way is to read each file into it's own HASHES OF ARRAYS data structure, then use Data::Comparator and Data::Dumper to display the differences between them:

use strict;
use warnings;
use Data::Comparator qw(data_comparator);
use Data::Dumper;

my $file1 = <<EOF;
Cell: AND1
A1 A2 Y
Cell: INV1
A Z
EOF

my $file2 = <<EOF;
Cell: AND1
A B Y
Cell: INV2
A Z
EOF

my $fh;
my $cell;

my %lib1;
open $fh, '<', \$file1 or die "Can not open file: $!";
while (<$fh>) {
    chomp;
    if (/ ^ Cell: \s+ (.*) /x) { 
        $cell = $1;
    }
    else {
        my @ports = split;
        push @{ $lib1{$cell} }, \@ports;
    }
}

my %lib2;
open $fh, '<', \$file2 or die "Can not open file: $!";
while (<$fh>) {
    chomp;
    if (/ ^ Cell: \s+ (.*) /x) { 
        $cell = $1;
    }
    else {
        my @ports = split;
        push @{ $lib2{$cell} }, \@ports;
    }
}

my $diff = data_comparator(\%lib1, \%lib2);
print Dumper($diff) unless ($diff->is_empty());

__END__

$VAR1 = bless( {
                 'AND1' => bless( [
                                    bless( [
                                             bless( do{\(my $o = 'A')}
+, 'Data::Differences' ),
                                             bless( do{\(my $o = 'B')}
+, 'Data::Differences' )                                           ], 
+'Data::Differences' )
                                  ], 'Data::Differences' ),
                 'INV2' => bless( do{\(my $o = [
                                      [
                                        'A',
                                        'Z'
                                      ]
                                    ])}, 'Data::Differences' )
               }, 'Data::Differences' );
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