This started happening in the last few days.
Usually my workflow is:
Alt + Click to select one or multiple parts inside of a model → RMB to open context menu → Union/Insert Object etc
This will make the operation occur for the selected parts.
Recently this behavior changed, RMB will cause the selection to change to whatever thing that is a direct child of the workspace under the mouse and then open the context menu. Basically just what happens when you just use LMB without Alt.
I don’t think this is an intended change (but maybe it is? it breaks my personal workflow anyway 
).