This is kind of a bizarre scenario, but I thought I'd document it, in case anyone else runs into a similar issue, since I wasn't able to find it through a Google search.
One of our users ran into an issue with saving a file and then suddenly (or shortly afterward) having the same file (with a 2 or 3 appended to its name) appear. In other words, if the file was originally called When Harry Met Sally, saving would then produce another file called When Harry Met Sally 2.
It appeared that iCloud was syncing it up to iCloud Drive, thinking that a local copy didn't exist, and then bringing back down the saved copy. Finder would then see that the file with that name already existed and then append a number to the name to distinguish from the original.
The solution was to move the file out of iCloud Drive (e.g., the Desktop folder), confirm to iCloud that the file was "deleted," and then move the file back. It would do a fresh sync with iCloud Drive and then behave properly.
Update 31 August, 2016: Unfortunately, it seems that fix was only temporary, and the behavior reverted. I'll see what else I can find. Seems I was able to find one more instance of someone else experiencing this—unfortunately, the solution was the same as what I described above.