I'm working with R15 and I'm getting the same behavior as you. I think you are correct that it's picking up the face or feature instead of the part node.
Personally, I find that selecting parts and features from the tree seems to work better than selecting in the graphics area.
But I have something you can try: Other Selections
1. right-click on the part geometry
2. choose the Other Selections option to display a little panel
3. right-click the part to be deleted (it's probably the 2nd item in the list, unless you have several levels of sub-assemblies)
4. now you can choose the Delete option
This is a couple more clicks, but everything can be done with the mouse and you don't have to search through the tree to find the part.
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