Defect tracking is the one feature that behaves most like I would expect and I have found a good way get it to work for me.
The features I use the most are the Test Planning, Test Set, Defect, and Defect Suite functionality. The Project Manager has stated multiple times that the reporting features of the User Stories & Sprint Planning work well for him. Though, like every other piece of the app, there are things that either do not make sense or have to be worked around to utilize the system as needed.
The Defect Tracking of CA Agile Central functions well enough with some severe limitations. I believe the intention is for you to put Defects in Defect Suites and Defect Suites in Iterations. You can put Defects in User Stories, but only one User Story at a time. So, if the defect crops back in, you either create a new defect or pull the defect from the previous sprint's User Story, thus changing history.
If you put them in Defect Suites you can add the same Defect to multiple Defect Suites in different Sprints. However, this also comes with some weirdness in removing a Defect from a Suite. You can't pull the Defect from the Suite directly, you have to go to the Defect and remove the Suite from there.
There is a Notes section for each of the Defects. Unlike JIRA there is no way to keep straight who made what comment when in the notes section. You have to manually add your name and date and time to the notes field making it so that if you have a back and forth about the root cause of the defect there is no ease way to facilitate this on the defect itself.
If one defect is causing failures in multiple Test Cases you cannot tag multiple Test Cases in the Defect. You either have to create multiple defects or note in the result that it failed because of the defect.
Test Sets & Test Plans, again, ALMOST function how you would expect. You can fairly easily lay out Test Cases in a Test Plan, unless you want to move a Test Case from one Test Folder to another, then you have to do so from within the Test Case rather than on the Test Plan page. You can move an entire nested Test Folder from one Test Folder to another. Deleting of a Test Folder orphans all the Test Cases making you have to hunt them down manually for deletion.
Test Sets are the method by which it appears you're supposed to keep execution results separate. Unfortunately, there is no way on the Test Plan to choose a Test Set to see the results. Test Plan only reports the latest results with no easy way to view historic execution results by Test Set. You also cannot view a Test Set's results independently. Further, adding Test Cases to a Test Set requires looking them up by Test Folder from the Test Plan. If the Test Folder has nested Folders, you can't search for the Parent Folder and add all Test Cases in the child folders. You can only create Test Sets in the Iteration, not in the Quality > Test Suites and then assign to an Iteration. Yes, It's called a Test Set and a Test Suite in the application.