There are a few potential causes for dirty water in your carpet cleaner.  One is that the water may be contaminated with dirt, dust, and other particles. Another possibility is that the water is not hot enough to kill bacteria and fungi. A third possibility is that the filter is not working properly. If you notice dirty water appearing on your carpet after your cleaner has been run, it might be a good idea to check to see if one of these issues is causing the problem.