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If you feel the issue is specific to our installation, you should file the issue in the koumbit issue tracker, always looking first if the issue was reported in the tracker. You should also look if it is a known bug on Drupal.org, in the general tracker.
If you feel it's an issue that is not specific to our installation, report the issue upstream, again after looking through the existing issues. There are 4 different projects for now in the Aegir project. You should generally file issues in the hosting module (the frontend you are generally using). If the error occurs in the backend (the tasks), that is part of the provision module. If it is a theming issue, that is the Eldir theme. When in doubt, file the bug in the hostmaster profile and upstream will reclassify the issue appropriately.
When in doubt regarding the responsibility, file the bug in our tracker and we will escalate it upstream if necessary.