So I've made one of these before but I've run into some problems on some new maps.

One of them I've gotten to the borders phase and it's all been fine except for making the actual borders. I've got the lines, I've snipped them off from the ocean. However, when I try to select a country I've set aside, it gets the entire island. (The world is made up of a lot of closely interconnected islands, basically.) It doesn't seem to identify that I've formed a border. It ignores the line I've drawn and just chooses the whole island.

Any ideas on how to fix this?