Adetque:

I don't see a way for a newline to be in your list. However, it looks like you'll get an empty string in your hash: You read the file with a newline, the newline is ignored, then you hit the end of the file. So $currentWord is "", which doesn't exist in your hash, so it's added. You'll probably want to verify that $currentWord isn't empty before stuffing it into your hash.

Having said that, though, I think I'd just use split to get your list of words and enter them into the hash--something like this (untested):

sub readWords {
    ## Gets how many of each word are in a file and returns a hash
    my $file = shift;
    my %words = ();

    # What characters to ignore
    my $blacklist = qr{[\s~`!@#\$%\^&\*\(\)\{\}\+=\\\/\[\]\.\,<>\?;:"]
++};

    open(my $FILE, "<", $file) or die("$0: $file: $!\n");
    while(my $currentline = <$FILE>) {
        $words{$_}++ for split $blacklist, $currentline;
    }
    close($FILE);
    return %words;
}
[download]

...roboticus

Update: I just tested the function and it works. A couple observations, though:

• You're returning a hash, but you may want to consider returning a hash reference instead.
• Your blacklist still allows some non-word characters in it (e.g. ' and _). You might want to use:
     my $blacklist = qr{\W+};
• The function allows an empty string to be added, so you might want to add (before the return statement):
     delete $words{''};