I have been doing a course that I already finished earlier, with lots those "changed" skills and almost all of the skills being considered "complete" except one last skill that wasn't originally there when I did this course for the first time.
To clarify: I finished this course a few years ago before all the updates when we still had "trees" and before the "path" was introduced. On a tree all of my skills were shown as "complete" while on a path they all were shown as incomplete and I could only access them one by one from the very beginnig till the end of the path, apparently in different parts of duolingo backend the same skills were considered both complete and incomplete simultaneously.
So, when I was doing the already "completed" skills the app kept telling me that I learned +15 ... +25 new words, while the data was only showing +1 or just a couple of words occasionally and it finally showed +14 only on that last new skill that wasn't originally there in the tree so I didn't do it earlier.
I suppose it probably means that for all the skills that I completed earlier most of the words were already counted back then, and while I was doing them again this time even though the app was showing +15 ... +25 (the full amount of words in those skills) duolingo was counting only newly introduced words, if any.
It's probably the same when duolingo said that you learned 12 words but 9 of them didn't count - those 9 are probably already in there in the total.