Could you tell us what your wordpress_sites has for subtree_path? I’m guessing you have something like this:
subtree_path: /
If that’s what you have, and you haven’t adjusted your project structure to be like the example project, you can just comment out subtree_path for both your sites, then redeploy. It is commented out by default.
Trellis has some checks in place to handle trouble with subtree_path, but I think it probably doesn’t currently handle the scenario of subtree_path: /, which may cause the problem you’re having.