#!/usr/bin/perl
use strict;
use warnings;

my $string = 'This is string';
my $capture1 = substr $string, 6, 2, "is stretched"; # This will substitute as expected

# REALLY?

print $string,"\n";

#  I get:
#  "This iis stretchedstring"

# perhaps better is:
my $string2 = 'This is string';
$string2 =~ s/string/streched string/;
print "$string2\n";

#  that prints:
#  "This is streched string"

# Your second substr():

substr $string, 9, 6, 'STRING';
print $string,"\n";

# that prints:
# This iis STRINGhedstring

# I suspect that you want:
$string2 =~ s/string/STRING/;
print "$string2\n";

# that prints:
# "This is streched STRING"