When looking in "All My Files", I see multiple instances of the same file In finder (OS X 10.12), when browsing the "All My Files" section I see usually 3 instances of each file. Even after deleting the real file the duplicates exist, and Finder tells me they are all the same size.

When I try to move these duplicates to my trash can, it turns into a eject symbol and I cannot delete them.
Do you have an external (or network) Time Machine drive set up? If so it is possible that you are seeing the backed up copies of your files.

Open System Preferences and click on the Spotlight icon and then the Privacy tab. Click the "+" button at the bottom of that window and add the Time Machine drive(s). You can then quit out of System preferences.

Something similar was happening to me where I was getting seemingly duplicate items in searches. Excluding my Time Machine drive eliminated that issue.

Just realize that now if you need a file from a Time Machine backup you cant just search for it, you'll have to enter Time Machine to find the file.