while ( my ($punctuation, $count) = each(%wordHash) )
{    
    $wordArray[my $i] = "$count\t$punctuation";
    $i++;
    print ("$count\t$charnames{$punctuation}\n");
}
[download]

Each time round that loop, you create a new variable called $i which is uninitialised (and therefore contains "undef"). You then use that variable as an array index. As it contains "undef", Perl converts it to a zero, but warns you that it has done so. You then increment the variable and let it go out of scope. A new (undefined) $i is created the next time round the loop.

What you probably want is this:

while ( my ($punctuation, $count) = each(%wordHash) )
{    
    push @wordArray, "$count\t$punctuation"
    print ("$count\t$charnames{$punctuation}\n");
}
[download]

Had you looked at the contents of @wordArray, you would have seen the problem.