I played around for a bit and did a bunch of cleanup. I'm not sure if this does exactly what you're after, but it shows a much better structure that you should be able to follow.

The biggest thing is that I got rid of all the variable definitions near the top. It's much easier to troubleshoot when you declare your variables immediately before use where possible.

This code surely needs more work, but I did what I could with the time I had. Also note that it doesn't look like you use @networklist, but I left it in anyways.

use strict;
use warnings;
use XML::Simple;

use Data::Dumper;

my $xml = do {local $/='';'in.xml'} ;
my $servers = XMLin($xml, ForceArray => 1);
my %seen;

my @networklist;
my @brlist;
my @vlist;

for my $server (@{$servers->{server}}){

    my $node =  $server->{NodeName__1};
    my $lanip = $server->{CoreLanIP_1__1};
    my $mask = $server->{CoreLanNetmask_1};

    my $network = join("/", $lanip, $mask);
    $network =~ s/.[0-9]*\//.0\//g;

    push @networklist, $network if ! $seen{$network}++;

    if ($server->{BRLAN} eq "y" ){
        core_lan($server);
    }
    else {
        core_vlan($server);
    }
}

# output

print "\nBRNW LIST\n";
print Dumper \@brlist;

print "\nVLAN LIST\n";
print Dumper \@vlist;

exit(0);

#
# subroutine definitions
#

sub core_lan {

    my $server = shift;

    my $brip = $server->{BR_IP};
    my $num = $server->{CoreLanNum};

    for (1..$num){
        my $corebrip = $server->{'CoreLanIP_'.$_.'__1'};
        my $brmask  = $server->{'CoreLanNetmask_'.$_};

        if ($corebrip eq $brip){
            my $brlist = join ("/", $brip, $brmask);
            $brlist =~  s/.[0-9]*\//.0\//g;

            push @brlist, $brlist unless $seen{$brlist}++;
        }
        else {
            print "coreip doesnot matches brip\n";
        }
    }
}

sub core_vlan {

    my $server = shift;

    my $brip = $server->{BR_IP};
    my $vnum = $server->{CoreVlanNum};

    for (1..$vnum){

        my $vlanip = $server->{'CoreVlan_IP_'.$_};
        my $vmask  = $server->{'CoreVlan_Netmask_'.$_};

        if ($brip && $vlanip eq $brip){

            my $vlist = join ("/", $brip, $vmask);
            $vlist =~  s/.[0-9]*\//.0\//g;
            push @vlist, $vlist if ! $seen{$vlist}++;
        }
    }
}
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