Honestly, in a game about ninja, can you really be mad if a ninja is a spy? He's a ninja... that's kinda what they do.

If you are afraid if a ninja is a spy, then spy on the other group and find out? Honestly, I know it feels underhanded, but there is no way to be sure you have removed the spy other wise. If you go on a witch hunt within your own group, you will only cause panic and make your ninja trust each other less.

In most cases, your spies are people who were originally trust worthy, but got tired of someone else in your group. If you can make your group a cool place too be where everyone feels like they have each others back, you will have less worries about spies. We had a spy in our group once, but after we won a war he came clean, and dropped his original group to join us because we were more fun.

Aside from that, moving your zones last minute or PMing you most trusted with where you want them to move to. you can take an entire zone of ninja and drop them on another zone by clicking on the name of the zone and dragging it too another... not sure if you already knew that.

anyways good luck