That looks wrong to me because it removes more than three lines.

Does this look correct?

#!/usr/bin/perl

use strict;
use warnings;

# Given an ini file, return a string containing section contents.
# (Note that ini file comment lines start with a ;)
sub get_section
{
   my $fcontents = shift;    # in: ini file contents string
   my $section   = shift;    # in: section name to get

   # Note that the regex below will find multiple sections;
   # it's terminated by the start of a new section or end of file.
   my $s = join( "", $fcontents =~ /^[ \t]*\[$section\](.*?)(?:\Z|^[ \
+t]*\[)/msg );

   $s =~ s/^[ \t]+//mg;    # remove leading  whitespace from each line
   $s =~ s/[ \t]+$//mg;    # remove trailing whitespace from each line
   $s =~ s/^\s+//;         # remove leading  whitespace
   $s =~ s/\s+$//;         # remove trailing whitespace

   # Remove up to three trailing comment lines
   $s =~ s/ ( \n (;.*)? ){1,3} \z //x;  # hopefully less of an eyesore

   return $s;
}

my $inifile_contents = <<'BUK_LIKES_SUNDIALS';
[MySection]
; This is a comment line for MySection
fld1 = 'value of field 1' 
fld2 = 42
; comment 1 inside the section
; comment 2 inside the section
fld3 =89
; trailer
; trailer 2
; trailer 3
; trailer 4
; trailer 5

; This is the heading for AnotherSection
[AnotherSection]
; another comment
asfld=69
BUK_LIKES_SUNDIALS

my $section1 = get_section( $inifile_contents, 'MySection' );
print "This is the contents of MySection -------\n$section1\n";

my $section2 = get_section( $inifile_contents, 'AnotherSection' );
print "This is the contents of AnotherSection -------\n$section2\n";
[download]

which prints

This is the contents of MySection -------
; This is a comment line for MySection
fld1 = 'value of field 1'
fld2 = 42
; comment 1 inside the section
; comment 2 inside the section
fld3 =89
; trailer
; trailer 2
; trailer 3
; trailer 4
This is the contents of AnotherSection -------
; another comment
asfld=69
[download]