couple general suggestions:

• use strict; At first, it'll generate a bunch of errors for you for undeclared variables, but it will help identify & reduce errors.
• Add some debugging statements. (Data::Dumper can be quite helpful, too)
  e.g. the warnings indicate that one of the values it's trying to add to the sum is a string .. so in the first for loop put something like print Dumper  [$i, $fields[$i]] if $fields[$i] =~ /s/;

Hmm .. actually, it might be your split -- try split(' ') instead -- see the split() docs for full info, including that "split(/ /)" will give you as many null initial fields as there are leading spaces. so it could be that your data file has leading spaces in it somewhere.

Here's a little refactoring example, too, to demo several more "perlish" constructs:

#!/usr/bin/perl -w
use strict;
my @sum;
my @sumsq;
my $n = 0;
while( <DATA> ){
  my @fields = split / /;
  foreach my $i ( 0..$#fields ){
    $sum[$i] += $fields[$i];
    $sumsq[$i] += $fields[$i]**2;
  }
  $n++;
}
$_ /= $n for @sum, @sumsq;
my @stddev = map { sqrt( $sumsq[$_] - $sum[$_]**2 ) } 0 .. $#sum;

print join(" ", @stddev) . "\n";

#foreach my $i ( 0 .. $#sum ){
#  printf "%5s %10s %10s\n", $i, $sum[$i], $stddev[$i];
#}

__DATA__
1.8 2.5 3.8 1.9 -3.5 -3.5 3.2 -3.9 4.2 4.5 2.8
-1.3 -0.9 -0.7 -0.4 -0.8 -3.5 -3.5 -1.6 -4.5
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