What did you expect? Remove the strange substitution and your processing seems reasonable. (Your logic is unnecessarily complicated, but it seems to do what you ask.)

use strict;
use warnings;
#my @array1 = `cat $ARGV[0]`;
#my @array2 = 'cat $ARGV[1]';
my @array1 = ("BIG_TREE\n");
my @array2 = (
    ' DATA: CREATE TABLE TEMP.BIG_TREE ;',
    ':',
    ':',
    '-------', 
    'foo',
);

my $read01 = 0;
foreach my $i (@array1) {
    for (@array2) {
        chomp($i);
        $read01++ if $read01;
        #s/./ . /g;
        if ( /CREATE TABLE TEMP\.$i/ ) {
            $read01 = 1;
        }
        $read01 = 0 if (/^----/);
        next if ( $read01 == 1 );
        next unless $read01;
        print "$_";
    }
}
[download]

OUTPUT:

::
[download]

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