NOTE: If you are running TuneUp 3.0 or higher, this support item is no longer valid. All support documentation for 3.0 and higher can be found under TuneUp Support - Learn More.
Bug: After DeDuping songs within your music library, TuneUp does not remove the track aliases within iTunes.
Workaround: Follow these instructions to rebuild your music library and remove any dead tracks left by TuneUp (or otherwise).
Fix ETA: While this bug is currently being worked on by our development team, we do not have an ETA to provide at this time.