For example, i never had rogue agents spawn at Ivy Tunnel controlpoint or The Choke, but Cinderblock or Haunted House quite frequently.
They're random. I've had them pop up at Ivy Tunnel and The Choke a couple of times.
They will spawn anywhere. Just an RNG type thing.
I think there might be some kind of timer on them, as in after x amount of playtime they've a chance to appear in missions, at control points or just turning up as you leave a safe house.
Places i have run into them a lot Sink hole, The Vault and overgrown as well or what it is called. However as others have pointed out they spawn randomly for the most part i have just run into them a lot at Vault for sure and Sink hole as well.