Here is my list of the weirdest issues I have experienced with SharePoint Online. Some of them are also reproduceable on-prem, some are not. I don't know if these are bugs or "by design" issues.
List with unique permissions in App Web
Did you know that if you want to have list with unique permissions in an App-Web (being part of an Add-In deployment), you must ask at least the Manage List permission in the App Manifest.