OK, I can't read your code easily, and I don't really feel like trying. If what you want is "all lines found in file1 which are not in file2" then here you go:

#!/usr/bin/perl
use strict;

my ($source_filename,$exclusion_filename) = @ARGV;

# read each line of exclusion file and store as a hash-key (for quicke
+r look-up)
open EXCLUSION, "$exclusion_filename" or die "Could not open file of e
+xcluded lines: $!\n";
my %exclude = map { ($_ => 1) } <EXCLUSION>;
close EXCLUSION;

open SOURCE, "$source_filename" or die "Could not open source file: $!
+\n";
while (<SOURCE>) {
    print unless $exclude{$_};
}
close SOURCE;
[download]

Results:

[me@host scratch]$ cat > a
asdf
asdf
fdsa
asd
ddd
d
[me@host scratch]$ cat > b
ddd
as
[me@host scratch]$ perl tmp.pl a b
asdf
asdf
fdsa
asd
d
[me@host scratch]$
[download]