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091005. Recently deleted var/cache/index so not a problem of old indices. "Dependencies in Java Tasklist" = "Enabled". I was working on apisupport.project and looking at SuiteCustomizerLibraries.Enabled, which was package-private. Find Usages claimed all usages were inside SuiteCustomizerLibraries.java, so I made it private. No error badges appeared in the Projects tab so it looked good. Later it turned out SuiteCustomizerLibrariesTest.java used this class; when I navigate to and open this class, suddenly error badges appear on it.
Easily reproducible; try adding and removing private modifier, even with both files open in the editor. The error badge on the test does not update until you switch to the test source, and warnings from IncorrectErrorBadges are shown in the log: WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Incorrect error badges detected, file=/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Going to recompute root=/space/src/nb/core-main/apisupport.project/test/unit/src, files in error=[]. WARNING [org.netbeans.core.TimableEventQueue]: Still previous controller org.netbeans.modules.profiler.actions.SelfSamplerAction$Controller@f054e2 WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Incorrect error badges detected, file=/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Going to recompute root=/space/src/nb/core-main/apisupport.project/test/unit/src, files in error=[file:/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java]. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Incorrect error badges detected, file=/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Going to recompute root=/space/src/nb/core-main/apisupport.project/test/unit/src, files in error=[]. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Incorrect error badges detected, file=/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java. WARNING [org.netbeans.modules.java.source.tasklist.IncorrectErrorBadges]: Going to recompute root=/space/src/nb/core-main/apisupport.project/test/unit/src, files in error=[file:/space/src/nb/core-main/apisupport.project/test/unit/src/org/netbeans/modules/apisupport/project/ui/customizer/SuiteCustomizerLibrariesTest.java].
Are you able to reproduce on a newer build? I tried, but did not really succeed. Quite likely duplicate of issue #173876. Thanks.
Can no longer reproduce in a dev build.