Ah, but the only reason for the flag is to immediately skip to the next iteration of the while loop, which can be done without a flag at all:

  FILE:
    while (defined(local $_ = readdir(LS))) {
        foreach my $file (@$exc) {
            next FILE if ($_ eq $file);
        }
        my $file = $dir . $_;
        my $append = "tar -rf $tarfile $file 2>> $ERRORFILE";
        system($append);
        print "\t$file\n";
    }
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Although I would use a hash for the excludes, instead of looping over an array for each file in the directory, especially since the most common case of a file not being in the exclude list would also be the slowest case.

I also recommend testing the readdir() assignment with defined, as I did above, so that the while loop will not stop prematurely if there's a file named '0'.