OK - which updates? Some updates need to be updated separately. For example, a security update issued yesterday may rely on an update issued last month to have already been applied. If having issues, try installing updates in batches of roughly a weeks worth and see if that helps.
Try to do the updates one at a time, until you find the particular one, or two, that will not install correctly. Some updates will not install becuase you already have a newer file or you do not really need it.