I cannot reproduce it with the trivial project configuration. Can you please provide your project or sample project
demonstrating this behavior?
Are there any exceptions in the log?

I can find dozens of 

Caused: java.lang.NoClassDefFoundError: org/python/antlr/ModuleParser
[catch] at org.netbeans.modules.python.editor.PythonParser.parse(PythonParser.java:116)
        at org.netbeans.modules.python.editor.PythonParser.sanitize(PythonParser.java:346)
        at org.netbeans.modules.python.editor.PythonParser.parse(PythonParser.java:93)
        at org.netbeans.modules.python.editor.PythonParser.parseFiles(PythonParser.java:315)
        at org.netbeans.napi.gsfret.source.Source.moveToPhase(Source.java:1064)
        at org.netbeans.napi.gsfret.source.CompilationController.toPhase(CompilationController.java:112)
        at org.netbeans.modules.gsf.GsfTaskProvider$Work$1.run(GsfTaskProvider.java:320)
        at org.netbeans.modules.gsf.GsfTaskProvider$Work$1.run(GsfTaskProvider.java:312)
        at org.netbeans.napi.gsfret.source.Source.runUserActionTask(Source.java:493)
        at org.netbeans.modules.gsf.GsfTaskProvider$Work.refreshFile(GsfTaskProvider.java:389)
        at org.netbeans.modules.gsf.GsfTaskProvider$Work.refreshFile(GsfTaskProvider.java:267)
        at org.netbeans.modules.gsf.GsfTaskProvider$Work.run(GsfTaskProvider.java:247)
        at org.openide.util.RequestProcessor$Task.run(RequestProcessor.java:577)
        at org.openide.util.RequestProcessor$Processor.run(RequestProcessor.java:1030)

for different *.py files (which I have reported with the exception reporter multiple times already). Note that I have
Jython project support installed.

Also I find messages like:

WARNUNG [org.netbeans.modules.java.source.parsing.JavacParser]: ClassPath identity changed for
C:\Users\moser\work\platform\modules\io\src\com\decodon\modules\io\FileMonitor.java, class path owner:
C:\Users\moser\work\platform\modules\io (class org.netbeans.modules.apisupport.project.NbModuleProject)
WARNUNG [org.netbeans.modules.java.source.usages.LuceneIndex]: Multiple index entries for binaryName:
Pair[com.decodon.apps.delta2d.autoupdate.SoftwareUpdateDialog$2,null]
WARNUNG [org.netbeans.modules.settings.convertors.XMLSettingsSupport]: Warning: unknown module code base:
com.decodon.modules.delta2d.ui in
C:\Users\moser\work\platform\suites\Delta2D\build\testuserdir\config\Windows2Local\Components\DualViewTopComponent.settings

I just have deactivated the Jython support. The exceptions are gone. But now I found

WARNUNG [org.netbeans.modules.java.source.parsing.JavacParser]: ClassPath identity changed for
C:\Users\moser\work\platform\modules\io\src\com\decodon\modules\io\FileMonitor.java, class path owner:
C:\Users\moser\work\platform\modules\io (class org.netbeans.modules.apisupport.project.NbModuleProject)

which is about the class I was searching usages for and

WARNUNG [org.netbeans.modules.java.source.indexing.JavaIndex]: Ignoring root with no ClassPath:
C:\Users\moser\work\platform\modules\delta2d-workflow\src\com\decodon\modules\delta2d\workflow

which is about the module with the missing usages.

thanks for investigating

In com/decodon/modules/delta2d/workflow there is either the class which is missing from the usages result list but there
are also some *.rb files. For those I have setup a Ruby project with the same package as src folder. 

That might have caused some conflicts: as a quick shot I also have deactivated the "Ruby and Rails" module, restarted
the IDE (with a clean var/cache, as always) and, voilá, Find usages on FileMonitor gives a complete result now.

reproduced 

Steps to reproduce:
1) create module A with class TestClass
2) create module B depending on A with class 
public class Tester {

    public void akce() {
	TestClass tc = new TestClass();
	tc.doIt();
    }
}
3) copy some .rb file under B's source root
4) create ruby project with existing sources, enter src folder from B as a source root (e.g.
/home/user/NetbeansProjects/ModuleB/src)
5) call find usages on TestClass in module A

Reassigning to ruby module after discussion with jpokorsky

Thanks for finding a reproducible use case. I don't think it is a common scenario to have two projects with the same
sources, so this scenario is probably a P3. Furthermore, the project infrastructure is built on the assumption that
every file belongs to <=1 project, so this is not really supported.
The question is, why are both these projects needed? Why is the Ruby project needed at the same time as the NetBeans
module project? Thanks.

I agree that for this scenario P3 is appropriate. 

However, the use case is valid: The platform module contains Java classes bridging some functionality provided in Ruby
scripts. Both the Java classes and the scripts tightly belong together, in particular an extra module for only the
scripts does not make sense.

Now, to profit from basic refactoring capabilities in a Ruby project, I want to view the scripts from a Ruby project
perspective. And I often switch between the Java and Ruby perspective in a session. So I definitely want to have both
projects open at the same time.

Thanks for explaining. Erno Mononen, who owns the Ruby area, is now on vacation, so let's wait until he comes back so he
can comment on this.

As Petr wrote before, this kind of setup (i.e. two projects with same sources) is unfortunately not supported at the 
moment. This should also not be necessary when we will have better Java/Ruby integration, including Ruby refactoring 
capabilities available in a Java project and vice versa. I'm afraid this may not be fixable for 6.8, but I'll take a 
better look at this still.