Sounds like you're trying to reimplement fgrep -v -F.

Here's a quick-and-dirty:

use Getopt::Long;
GetOptions( 'file=s' => \my $patfile );

chomp( my @del = do { local @ARGV = ($patfile); <> } );
my %del; @del{ @del } = ();

$, = $\ = $/;
print grep { chomp; not exists $del{$_} } <>;
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call it like so:

perl this_script.pl -f A < B > C
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(given A, B, C, per your root post)