Is $file a directory or a file? If you want to delete a directory, use rmdir (if it's empty) or rmtree in File::Path (if it's occupied). If you unlink a file, the error will be in $! (not $@). See perlvar. Finally, your warn refers to a $filename variable that isn't used anywhere else. Maybe what you're trying to do is:

my @dir = $ftp->($file);
if ( $dir[0] =~ /$size/ ) {
    unlink $file or die "Can't unlink '$file': $!";
}
else {
    warn "File size differs for $file ($size): $dir[0]\n";
}
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