I think the bottom perfs could be a cutting or tearing tool used to separate stamps from each other.
Perhaps a machine made for coil stamps or for strips of ordinary stamps?
In this photo I have taken the bottom perfs and flipped them topsy turvy and placed a snippet of them next to the upper perfs.
You can see the cutting teeth were positioned exactly where the original perf holes would have been if the vertical alignment was correct.

Just a mistake made when separating the stamps apart perhaps?