A lot of security concerns are not from the software themselves, but from the configuration surrounding the infrastructure. For example, consider a setup that has dozens or hundreds of instances, each with their own internal firewall configurations. Without the use of the configuration management software such as Puppet or Chef or a very fine process regarding this configuration, each instance may end up with a slightly different set of rules from the next.

Add to this example that the infrastructure itself may have similar configuration such as the AWS-provided Security Groups. With these many instances, it could get out of control very quickly if care is not taken from the beginning or is iterated over repeatedly. Some groups may conflict with others, cause gaps in protection, or just not work as expected. What started as a good process might evolve into a spider web of headaches.

One benefit of Security Groups is their flexibility: they can be stacked on top...