For the same reason that the Combine aren't actively trying to process every poor bastard left out in the outlands, the Combine wouldn't care about anywhere that isn't a significant population center. The humans outside of these centers will probably die due to the Combine's pollution, destruction of the ecosystem, or from Xen wildlife.
If they prove particularly hardy, while being counteractive enough to the Combine's operations to warrant it, the most they'll do is shell North Sentinel Island and call it a day.