Please post a self-contained, small example that reproduces the behaviour you see.

Using the below code, I cannot reproduce your problem:

#!perl -w
use strict;

my $sorce_direcrtory = '.';
my $new_directory = './target/';

opendir(my $dh, $sorce_direcrtory) || die $!;
while(readdir $dh) {
    print "Found directory entry [$_]\n";
    if($_ =~ /.csv/){
        print qq{copy("$sorce_direcrtory/$_", "$new_directory/$_")\n};
    }
}
closedir $dh;
[download]