Well guys, all is well now, as this was a self-inflicted problem. I can't believe I fell for this, but it happened.
Here is how.
1. I typed "Sierra" into Spotlight and clicked "Open in Finder".
2. I opened another Finder window to create a new folder and moved the file to it.
3. Guess what, the Finder window that Spotlight opens up is updated in real time, so every copy I made was popping up there under "Applications", regardless of the real file location.
4. You can see how this became a circular problem once I started deleting copies and they appeared to be deleting two at a time, even though that isn't what was actually happening.
5. When I was looking at the file info I should have paid more attention to the file location path, but I was focusing on the file size instead to rule out a file alias.
6. Basically, Finder was behaving like it was supposed to, I just wasn't expecting the result and focused in the wrong direction. My bad...Thanks for helping, it's always appreciated.