Collider not working as trigger when painted into the scene

I'm making a game were you have to hide from space ships as you collect parts. I want to be able to hide from these alien ships under the trees. I have added a sphere collider to the top of the tree and have changed it to a trigger, and am able to hide from the ships and still go through the tree tops. But after i make a new prefab and place it into the paint tree attribute to start placing the trees, the trigger no longer works and becomes a collider that i no longer can go through. i didn't have this problem when i had unity 4.6 but we updated to unity 5.3 and it no longer wants to work. if anyone has any ideas on how to have each tree be a trigger and react with our script, we could really use the help. Thanks