Don't forget the flow will determine by how much a population will exist. The default flow is .25, or 25%, which will still let populations inside of it (just a smaller then usual amount) Set the flow to 1 for 100%, then paint the areas you do not want your populations. This should make no populations show up.
Attached example: left is one stroke at .25, right is one stroke at 1. Note how .25 has a few stragglers around.
So double check you painted with 1.