Consider making slightly more use of your program's memory.

my %command;
my $destination;
while(<DATA>) {
    # assign split results to named scalars
    my ($ignored, $file, $flag) = split /,/;
    if ($flag =~ /^[CD]$/) {
        $destination = $file;
        $command{$destination} = "type $flag";
    }  
    $command{$destination} .= " $file.txt";
}
for my $destination (sort keys %command) {
    # Look, only one print statement!
    print "$command{$destination} > $destination.txt\n";
}
__DATA__
IM,BEN01,D,0
IM,BEN02,D,0
IM,BEN03, ,0
IM,BEN04, ,0
IM,BEN05, ,0
IM,BEN06,C,0
IM,BEN07, ,0
IM,BEN08, ,0
IM,BEN09, ,0
IM,BEN10,D,0
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