I think its safe to say the problem lies in Aptoide and how it goes about providing updates since this is a open sourced app and community.
Best you can try is going into Settings/Apps/Manage Apps and find the apps in question and see if you are given the option to uninstall the updates. Otherwise you maybe forced into deleting the entire app using Titanium Backup or some other means to get it off the device and start over.
Just my opinion but best to stick with Google Play Store, Amazon, Get Jar or Slide Me for your application needs.