The reason you're getting no results is because your comparison is the wrong way around :). You are checking to see if the word matches the regex with the entire 2nd phrase instead of the other way around.
I've taken the liberty of changing a few other things (sorry, couldn't resist). Amongst other things, the changes are in

• how you load the file contents
• how you remove special characters (and when)
• how you loop through the words
• how you keep track of the match_count
• and how you perform the match

use strict;
use warnings;
use v5.10;

my @data = <>;

my $match_count = 1;
foreach my $line (@data) {
    chomp ($line);
    print "Processing line [$line]\n";
    $line =~ s/[",\/-]/ /g;    # Change all potential word endings to 
+a single space
    $line =~ s/[()]//g;        # Remove parentheses to avoid mishaps d
+uring pattern matching
    my ($id, $source, $comparison) = split "\t", $line;    # Split col
+umns into an array
    foreach my $word (split ' ', $source) {
        given (length $word) {
            when ($_ < 3) {
                next;
            }
            when ($_ < 5) {
                if ($comparison =~ /$word/i) {
                    print "Match [$match_count] (probable): [$word]\n"
+;
                    $match_count++;
                }
            }
            default {
                if ($comparison =~ /$word/i) {
                    print "Match [$match_count]: [$word]\n";
                    $match_count++;
                }
            }
        }
    }
}
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