Well, without seeing your html and txt files, it's impossible to say for sure, I tried this with the following:

template.html:
<H>%%insert_here%%</H>
sldfjkdslkf
sdlfkjsdlf
sldkjfdslk
<B>%%insert_here%%</B>

data.txt:
hello

foo.html:
<H>hello
</H>
sldfjkdslkf
sdlfkjsdlf
sldkjfdslk
<B>hello
</B>
[download]

I will tell you however, that you'd be doing well to code it a little more like

use strict;
my $htmlfile = "template.html";
my $datafile = "data.txt";
my $outfile = "foo.html";

my @cat1 = `/bin/cat $htmlfile`;
my $cat2 = `/bin/cat $datafile`;

open(OUTFILE, "> $outfile") || die "Can't open $outfile for write: $!"
+;

foreach my $line (@cat1) {
     $line =~ s/%%insert_here%%/$cat2/ge;
     #maybe
     print OUTFILE "$line\n";
}

close(OUTFILE);
[download]

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