When you create a copy of master page and load it again, by default visible is set to false for DeltaPlaceHolderLeftNavBar tag as shown below.
- <SharePoint:AjaxDelta id="DeltaPlaceHolderLeftNavBar" BlockElement="true" CssClass="ms-core-navigation" role="navigation" runat="server" visible="false">
Please set it to false or remove visible="false". Now you would be able to add sharepoint app without any more issue.
Happy SharePointing.