use strict;
use warnings; # you left this out

my $file = "controls.txt";
open (my $fh, '<',  $file) or die "Can't open $file for read: $!";
# Don't use two-arg open unless you know why, and use
# lexical filehandles unless you know of a reason not to.

my %seen;
while ( <$fh> ) {
  $seen{$_} = 1;
  # Later assignments to an identical key
  # overwrite earlier ones, so there's really
  # no need to check if all you want is uniqueness.
}

my @unique = keys %seen;
print @unique;