Following compiler error is produced under following circumstances:

./test/p3/C3.java:1: error: unnamed package is not allowed in named modules
package p3;
^

The circumstances are:
1. Compilation is performed via JSR199 API.
2. StandardJavaFileManager instance is retrieved and used in compiling in module mode, that is when -modulepath and -modulesourcepath options are specified.
3. The same StandardJavaFileManager instance which was used in step 2 is used for compiling in NON module mode, that is when -classpath option is specified and -modulepath and -modulesourcepath options are not.

The 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/Test31/test.sh by setting JDK_HOME variable to your JDK installation dir.
3. Run A/Test31/test.sh.

These steps produce following output on JDK 9 build 130:

With the same file manager:
Compilation in module mode succeeded
./test/p3/C3.java:1: error: unnamed package is not allowed in named modules
package p3;
^
Compilation in NON-module mode failed

With fresh file manager:
Compilation in NON-module mode succeeded