Here is one way:

use warnings;
use strict;

my $flag_count = 0;
while (<DATA>) {
    $flag_count++ while /<BEGIN_FLAG>/g
}
print "flag_count = $flag_count\n";

__DATA__
<BEGIN_FLAG> foo
bar
goo <BEGIN_FLAG> boo <BEGIN_FLAG>

__END__

flag_count = 3
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