Along with what bm said, it looks like you're forgetting to chomp off any newline characters.

use strict;

my %count;

while( <DATA> ) {
    chomp;
    $count{ $_ }++;        
}

print "$_\t$count{ $_ }\n" for keys %count;

__DATA__
123  56
123  56
234  45
123  56
678  93
678  93
[download]

With chomp:

678  93 2
234  45 1
123  56 3
[download]

w/o chomp:

678  93
        1
678  93 1
123  56
        3
234  45
        1
[download]

--
"To err is human, but to really foul things up you need a computer." --Paul Ehrlich