The problem is that a small handful of programs are poorly designed and recreate their useless shortcuts and registry keys when they see that they have been removed.
Therefore it is almost impossible to be completely error-free. In addition a low amount of this type of errors has no real influence on the performance of the system.
We recommend a scan and repair with NovaTuneUp once or twice per week, and every time twice in a row, to keep the system optimized.
Try to look in the task manager after running a scan and repair. You'll see all the open processes you have. So even though it feels like no action has been taken, loads of processes has been running with the possibility of creating errors.