Also, a nice thing to keep in mind is checks and balances.
Let's say you have a legion of hobgoblins in Area X. They are hyper-vigilant about patrolling their areas, and nip any monsters in the bud. If the PCs sweep in and wipe out the hobgoblins, then whatever the Hobs have been keeping at bay start to crop up.
Another idea is "This monster is extinct/on ice". Take for example... carrion crawlers and chuuls. These things may have died out long ago. However, there are eggs buried in sealed caves that, when re-opened, cause them to re-emerge in this one area. (Think: Alien).