I've been getting this odd issue lately with the Public folder being created outside of the root folder structure. I've done a few different tests with it and can't really seem to point my finger on the cause. It happens when I run 'roots watch' and I'm not sure if it's because of certain project names or what.
For instance: I ran a 'roots new mobile' and this issue occured. However, running 'roots new mobileportfolio' worked and functioned as normal.
Currently running MacOS Sierra 10.12.1 on the Late 2016 Touchbar MBP 13".