Example:

File: stat.h
struct stat {
   ...
}

jextract generates stat.java for header and "stat" inside it

// header interface
interface stat {
    ...
   // interface for struct stat
   static interface stat extends Struct<stat> {... }
}

The above is not valid code.
https://docs.oracle.com/javase/specs/jls/se11/html/jls-8.html#jls-8.1

"It is a compile-time error if a class has the same simple name as any of its enclosing classes or interfaces. "

Another name clash case:

/usr/include/sys/_types directory is mapped to usr.include.sys._types package. But there is a header called /usr/include/sys/_types.java which is mapped to header interface named usr.include.sys._types. i.e., a package and a class with the same fully qualified name. And that does not compile as well.