under unix shell 2>&1 redirects STDERR to STDOUT. If you then add a pipe you do indeed get the whole lot going down the pipe (so if this pipe then connected to a perl file handle you would be reading STDERR and STDOUT mixed together in Perl). Perl sends it's warnings to STDERR as this little test shows

# A simple perl script to generate a warning
: perl -we 'my $t; my $t'
"my" variable $t masks earlier declaration in same scope at -e line 1.
# the same with STDOUT redirected to null
: perl -we 'my $t; my $t' >/dev/null
"my" variable $t masks earlier declaration in same scope at -e line 1.
# same with STDERR to null, aaah the sound of silence
: perl -we 'my $t; my $t' 2>/dev/null
:
[download]

What may be enough for you is to check the exit code of the script you call (hopefuly it exits with 0 when it runs OK and non-zero values for failures

my $cmd="ls /no/way"; 
my @data=`$cmd`; 
if($?) {
    print "$cmd failed with exit code $?\n";
    exit 1
}
foreach (@data) {
    chomp;
    my @ret=split;
    # do something with @ret here ?
}
[download]

This is running the external script to completion first then checking it did not give an error code before going on to process the results.

Cheers,
R.