Collider not turning into trigger when painted to a 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

It looks to me as if you’re not the only one with the problem and that terrain trees work different from ordinary prefabs. In this post there’s a lot going on considering terrain and trees, maybe something in here is helpful for you: