This kinda is a spoiler.kinda. But did anyone else notice that the combine and xen creatures fight each other. Doesnt this kinda prove that they aren't controlled by some greater power,or somethin.
The Xen wildlife is the equivelant to our birds, dogs, etc. They got teleported in during the storm. It's the flora and fauna.
The Vortigaunts from Xen (sentient people) were under the control of Nihilanth by their collars (which they are free of now.) I personally believe Nihilanth was controlled by the Combine.
Also, you can see enslaved Vortigaunts to the combine. In the trainstation, one is sweeping the floor, and one in Nova Prospekt was tortured in a chair with a collar on and being used to power a force field.