Im not sure if its just our install or what but I've been fighting this problem for the last week.
Solution is to change Scope > Option > to Fully Load - Lightweight display"
I was using a check body from an assembly in the operation and as soon as you close the session you can no longer open that operation and you get the error because the check geometry was only "partially loaded".
I have seen this problem in Nx12 when using an existing master model part file as a template.
My normal workflow is to setup my geometry in my manufacturing assembly file by adding parts to the assembly and then initialise the CAM environment from my exisiting CAM file that I have turned into a template file. I have not worked out why but in some cases I am unable to select WORKPIECE geometry and in other cases AREA_MILL geometry and get the same error you are seeing - "The object contains geometry not in the current reference set".
My workaround for this is to initialise the CAM environment first and then add the parts to the CAM assembly. This has not failed for me.
had this happen to me today. load setting solved the issue.