I see two main problems.

First, the following lines are in the wrong order for what you want your output to be:

print "$command\n";
$exp->send("$command\n");
$exp->expect(1, '-re','\(\d+\)');
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You probably want this order instead:

$exp->send("$command\n");
print "$command\n";
$exp->expect(1, '-re','\(\d+\)');
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Second, this:

my $counter = 1;
print "($counter) ";
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Should just be this:

my $counter = 0;
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The extra stuff is just junk since you print and increment the counter in your loop. This change will fix printing 1 and 2 together like you observed here: (1) (2) Here is the second command

EDIT: Hmmm. Looking at your scripts more closely, I'm having second thoughts about this. What if you just print it all from the server script? Like this:

while (<STDIN>) {
  chomp;

  $counter++;
  print "($counter) $_\n";

  if ($_ eq "error")  {print "Error on command #$counter\n";}
  if ($_ eq "commit") {print "Committing data\n";}
  if ($_ eq "exit")   {print "Exiting program...\n"; exit;}
}
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