More or less, yes it is going to be a potential issue with the near real-time co-authoring provided by Office Web Apps/Office Online Server. Essentially, users have to save the document in order to see other's updates. In addition, if the document fails to upload from the Upload Center, it is possible that is why you're seeing deleted data reappear. For the conflicts, saving the document may cause those if someone has edited the same section.
Recommendation is switching to SharePoint Online which has real-time co-authoring and, in general, doesn't run into these issues.