Thank you for pointing out the problem and the workaround. I imagine you have noticed that some elements have an identically named sub-entry, while others do not. The ones that do correspond to actual files in the file system. The sub-entry is there to allow users to perform config management operations at this file level. While they should behave in the same manner, I recommend getting in the habit of using the context menu entries on the parent item and not the sub-entry item.
I also generally recommend that CM operations be performed from the project level. This will guarantee that any model changes that affect multiple files “stay together” so you don’t have data in the CM repository that isn’t all squared up.