I came across this partially peeling patch a few weeks ago, and took this photo, intending to share it when I got around to it. And lo and behold, R' Alberto Attia posts something similar: http://www.stamforum.com/2013/03/tzafun.html.
I was dan likaf zechus that this was from a scrap that was used to practice with. I don't see any reason that one would be required to think otherwise.
I would, however, debate the propriety of putting a matlis on top of a hole. Does anyone have a comment on that?
Now, if you will indulge me, I would like to dig deeply into the concept of a matlis with words:
If one were to make a matlis that merely covered a word of the sefer Torah without damaging it, would the Sefer Torah then be pasul? Assuming that it is pasul, if the matlis was then removed, would the Sefer then be kosher, or would it be chok tachos?
If you follow my line of reasoning, I would like to question if the presence of letters on the matlis, even when not visible can pasul the sefer Torah.
Perhaps it is for this very reason that the halacha is that a matlis for writing can only be placed behind; to avoid the problem of one putting a matlis on top of letters that are not removed.