Background:
Entire site collection uses a custom Master page located on top level.
Recent change:
Subsite permissions were changed to enable a particular group access to the subsite, but not top level site. So the subsite is no longer inheriting permissions and a new group was added with read rights to the subsite only.
Problem:
Master page on the subsite now displays wonky. Menus are listed down the left instead of layered, etc...
What am I missing?
When you broke the permission inheritance to the parent site, you also broke inheritance to essential style files, page layout files, and other essential files which define the page's structure, etc. These system files are located at the root of the site collection.
Your users should always have at least Read-permissions to the system files. As they have been given access rights only to the subsite-level, this requirement doesn't fulfill. Therefore, you need to adjust your user permissions.
Slightly offtopic, but a rule of thumb when designing a site collection is to consider the user groups that should access the particular site. It's always recommended to have a top-to-down architecture, where users always have permissions to the parent site of a subsite.
