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use strict;
use warnings;
...
    my ($site, $userID, $data) = ($1, $2, $3);
    print "SITE: $site   USER: $userID   DATA: $data\n";
}

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

  next unless $line =~ m{^(\S+) (\d+) (.*)};
  my ($site, $userID, $data, $data2) = ($1, $2, $3, $4);
...
  $user{$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

print Dumper \%user;