If you are searching for the words from file A in file B then you will need a different regex. The code you provided is using the entire file A as the regex.

Here's an example that uses one pattern file, one input file, one output file:

use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my @tokens = ();
while (my $line = <$pattern_fh>) {
    push @tokens, split /\s/, $line;
}
# Create a pattern with alternation of tokens, wrapped in a non-captur
+ing group,
# and a requires word break before and after the word to prevent match
+ing pieces
# of other words 
my $pattern = '\b(?:' . join('|', @tokens) . ')\b';
print "Search pattern: $pattern\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!"; 
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!"; 

while(my $line = <$infile>) { 
    if ($line !~/$pattern/) { 
        print "adding: $line"; 
        print $outfile $line; 
    } 
} 
close($infile); 
close($outfile);
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