I would try something more like this:

#!/usr/bin/perl 

use strict;
use warnings;
use Data::Dumper::Concise;

my(@array) = qw(
    1111599 AB563244.1 Streptococcus macedonicus str. W28             
+   
    1111215 AB563262.1 Streptococcus equinus str. MTS6
);

print Dumper( "Occur twice: @{numbers(\@array, 2);}" );

sub numbers {
    my ($newArray, $n) = (shift @_, shift @_);
    my(%count)= (); 
    my(@temp_arr) = grep( {$count{$_} == $n;} 
    grep ({++$count{$_} == 1;} @$newArray));
    print "\%count:\n";
    while ( my ($key, $value) = each(%count) ) {
        print Dumper( "$key => $value" );
    }
    return \@temp_arr; 
}
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