If you are opening the html file and reading into a scalar i.e.

use strict;
my $input = "somefile.html";
open (INPUT, $input) || die;
my $content = <INPUT>;
close INPUT;
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it will just pick up the first line in the file. Instead you want to either a) read the file into an array, or b) use LWP::Simple to get the page into a scalar i.e.

use strict;
my $content = LWP::Simple::get($input);
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elbow