use strict;
use warnings;

my @lines = (
'012345 NA13333 C C',
'012345 NA13334 F F',
'012345 NA13335 E F',
'012346 NA13333 U U',
'012346 NA13334 I I',
'012346 NA13335 Y O');

foreach my $line (@lines) {
    next unless $line =~ m{^(\S+) NA(\d+) (.*)};
    my ($site, $userID, $data) = ($1, $2, $3);
    print "SITE: $site   USER: $userID   DATA: $data\n";
}

##</code><code>##

SITE: 012345   USER: 13333   DATA: C C
SITE: 012345   USER: 13334   DATA: F F
SITE: 012345   USER: 13335   DATA: E F
SITE: 012346   USER: 13333   DATA: U U
SITE: 012346   USER: 13334   DATA: I I
SITE: 012346   USER: 13335   DATA: Y O

##</code><code>##

  next unless $line =~ m{^(\S+) (\d+) (.*)};
  my ($site, $userID, $data, $data2) = ($1, $2, $3, $4);
  # you have 3 capturing paran's but you try to call $4
  # your 2 data columns get folded together in $3 because of your greedy .*

  $user{$userID}{$site} = $data, $data2;
  # $data2 is useless and I think you are trying to use an array ref
  # but that is not what you are doing [ ] signifies an array ref

##</code><code>##

print Dumper \%user;