my $pattern_file = <STDIN>;
chomp $pattern_file;

open my $patterns, "<", $pattern_file or die "Can't open '$pattern_file' for reading: $!";
my @patterns = <$patterns>;
chomp @patterns;
@patterns = grep length(), @patterns;
@patterns = map qr/$_/, @patterns;

...

foreach my $file ( ... )
{
    # All patterns must match
    foreach my $pattern ( @patterns )
    {
        next if $file =~ $pattern;

        print OUT "'$file' !~ /$pattern/\n";
        last;
    }
}