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When selecting a working set as the filter for the problems view then the problems are sometimes not filtered correctly. This happens when the working set contains a large number (about 55) of selected packages. In this case the result isn't filtered at all.
i'm having a similar problem, so hopefully it's cool that i add my comments to maybe help the developers. i think this is a bug that has been around since i've tried 3.0 M7. i have a few packages that i would like to filter out of the problems view using a working set. these packages contain java source files that are automatically created by a tool. they have unneeded imports, so the problems view shows a lot of warnings. in 2.1, i would create a working set and set the filter in the tasks view. everything filtered as expected. in 3.0 M7-M9 & RC2, i create the same working set and try to filter the problems view. some of the files are filtered, but not all of them. package A, 105 java files, filter DOESN'T work package B, 110 java files, filter DOESN'T work package C, 3 java files, filter works package D, 3 java files, filter works it's strange that the working set filter works for packages C & D, but not A & B. the only difference i can see is A & B contain a lot of java files, and C & D don't. i don't think this should make a difference. i'm doing it the same way i did in the 2.1 tasks view, which worked just fine. now, with the 3.0 problems view, i have 200 warnings. this currently makes 3.0 unusable for me, since trying to find my "legit" problems in a list of 200 i want to ignore almost impossible.
I believe that what you're observing is the behavior reported in bug 8043: working-set filters currently filter based on physical directory structure rather than the logical structure of packages. When showing package a.b, you'll also see markers for packages a.b.c and a.b.d. *** This bug has been marked as a duplicate of 8043 ***
