When performing annotation processing on class files error presented below occurs. It's hard to say from this point what is the exact root cause of this error.
Minimized test case is attached, in order to reproduce the bug please:
1. Unzip attached archive to some dir, say A, on Unix/Linux machine.
2. Modify A/Test37/test.sh by setting JDK_HOME variable to your JDK installation dir.
3. Run A/Test37/test.sh.

On JDK9 build 131 it causes following output:

Root elemnts count: 3
Root class: p1.C
Root class: p2.A
error: cannot access Inter
  class file for p3.Inter not found
  Consult the following stack trace for details.
  com.sun.tools.javac.code.Symbol$CompletionFailure: class file for p3.Inter not found
Root elemnts count: 0
1 error