Hi,
There is on thing you can try, any item which you can not spy/highlight using application modeler, go to Application navigator and find the particular element, take a snapshot of its attribute displayed in application navigator, now go to Application modeler, spy the element, cross verify the properties shown in in Application modeler vs Application navigator(the snapshot you captured).
You will notice some difference like class name or id has nested elements(parent elements property + child element property), manually change them referring to the application navigator snap shot, try to highlight it, you should be able to highlight that now.