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
With chomp:
678 93 2
234 45 1
123 56 3
w/o chomp:
678 93
1
678 93 1
123 56
3
234 45
1
--
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