You're using capturing parentheses, which will cause the capture to be inserted into the split result (read perldoc split on this). Also, please use strict and use warnings, those would have caught a typo in $chunck1 as well as your incorrect use of the variable name $sectionname2 (where you actually mean $chunk2. Below a corrected version of your script

#!/usr/bin/perl

use strict;
use warnings;

my $chunk1;
my $chunk2;
my $chunk3;

{
    local $/ = undef;
    (undef,$chunk1,$chunk2,$chunk3) = split(/^!(?:sectionname1|section
+name2|sectionname3)$/m, <DATA>);
}

print $chunk2;

__DATA__
!sectionname1
this is the data
!sectionname2
this is more data
!sectionname3
end
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