Two recommendations -- neither of which goes to your current issue (answered well, above), but which may be important in some other context:

IMO (Caveat: my O is neither definitive nor authoritative), you rely too much on the default var, $_. Doing so, in the face of possible future needs for tweaking, extension, modification, or refactoring of your code can
  a) create a script-version that inadvertently replaces the content of $_ with something other than its current content... and
  b) make - for yourself or some future programmer - a head-scratcher about what's supposed to be in $_, once you're reading some lines down.

Changing your code (and code-writing practices) to use explicitly named vars for values you're passing around, hither-and-thither, is relatively low overhead -- while writing and when executing. For example, one could do this (your line numbers, my comments):

056: my (@words, $char, $vowel);
057: while (<$IN>) { 
058:     @words = split /[\W]/, ;
059:     for my $word(@words) {                         ## explicit va
+riable declared...
060:         print $OUT (encode ('UTF-8', $word)) . "\n";  ## and put 
+to further use...
061:         my $count = 0;
061a-061z:                              ## hypothetical insert, tweak,
+ extension, etc
062:         my $end = length($word);                   ## Ahah, easy 
+to verify that 
                                                       ## we're gettin
+g word length
063:         for (my $i = 0; $i < $end; $i++) {
064:             $char = substr($word, $i, 1);          ## and again..
+..
[download]

I also recommend that you consider advice seen often here; that you eschew using the &foo... form of sub call which precedes the sub name with an ampersand... unless you know * EXACTLY * why you need the ampersand. Summarizing that advice: "Don't, because using the ampersand when not needed can help you create bugs that are very hard to find... and because it probably doesn't do what you think it does."

Here's some additional reading:

• First, a canonical resource: Learning Perl - However, this links to 3rd Ed; you should use 5th edition, but 3rd is freely available on line; see {search for} "Omitting the Ampersand"
• Perl-Critic http://search.cpan.org/dist/Perl-Critic/lib/Perl/Critic/Policy/Subroutines/ProhibitAmpersandSigils.pm chimes in with this "description: 'Since Perl 5, the ampersand sigil is completely optional when invoking subroutines. It also turns off checking of subroutine prototypes. It's easily confused with the bitwise 'and' operator.'"
• https://www.socialtext.net/perl5/subroutines_called_with_the_ampersand -- Seems to me to be an excellent discussion (don't let the https: dismay you; it's openly readable)
• http://www.webreference.com/programming/perl/subroutines/ - don't stop reading after the first couple para: the meat re "&foo()" is well down in the text.
• Re: What is the point of the & sigil for function refs? - 6 years old, but still relevant for any 5.n version ...
• http://www.0x61.com/forum/programming-perl-f240/ampersand-subroutine-t1136804.html -- ...and there are a few worthy points in this thread
• http://www.devdaily.com/perl/call-perl-subroutines-sub-function-ampersand - an interesting perspective

hth