First off, I screwed up.
I reversed several directories in my project which did not place the elements in the correct packages. I move things around, but had duplicates and did know how to merge elements of the same type
Made the diagram in the screen shots
Later I deleted the packages made by the reversing. Apparently, one element referenced in the diagram was to an element in these packages.
Now, the next day, there are invisible elements on the diagram. They are still there, because I can select them. When you look at the properties, the classifier is empty. I tried to assign the correct classifier, but the program will not accept it.
Also, got an error trying to enable node debugger (see 4th screen shot).
1) If there is a reference to an element and the element does not exist, then the reference should be removed or the program should allow the user to assign a new reference.
2) An element in a diagram should never be invisible. If there is a problem then the program should display some kind image denoting the problem and provide a path for the user to correct it.