When you toggle zoom extents the program will display the total model with some parts you do not realize you made. It could be a very short line you cannot even see.
Suggest you select the model( double click), change the rendering mode to wire frame and hide it. Then do a select all and delete. Un-hide your model and then do the zoom extents again.
Hidden wire frame is not selectable so this will only delete the items you do not want. Save your model first, this works through Su8 I've not check if it is ok for 2013