We were able to identify the problem. Some labels of your graph contain invalid positions. As a result, the viewer cannot correctly calculate the bounding box of the graph and fit content fails.
This is a known problem with the SmartFree label model in yEd 3.9. It will be corrected in the next release. To fix your existing diagrams, it should be enough to change the label model (in the Label's Position setting) to Free. (To select all nodes, press Ctrl+A.)