The issue is not specific to registry keys. If you are using an uninstaller which creates snapshots before and after installing software, changes to both files and registry keys which do not belong to the program being installed can be monitored too. This is also a problem with uninstallers which just scan for leftovers are the normal uninstaller runs. On occasion, they will think that unrelated files and registry keys belong to the program that was just uninstalled.Hmm, this honestly puzzled me, even though roger_m mentioned that he did not experience any kind of convenience regarding the matter. Is there an option to not remove the registry keys but the rest?
In both cases, the best way to handle this, is to pay attention to what the uninstaller wants to delete and be sure to uncheck anything that is not related to the program your are removing.