You can suppress this node creation gesture using the settings.
When in Edit Mode, yEd will create a new node at the spot you click on the canvas. This can be irritating if you are used to creating specific node types with a drag and drop gesture from the palette. To disable node creation upon mouse click, open the preferences dialog from the menu [File]->[Preferences...]. On tab [Editor] uncheck the setting [Create Node on Background Click].
That's it.