uh oh... I think I responded to this... or did I not?
These notes are printed with block numbers, as they were the first series after WWII and when Japan chronically needed small change.
The serial numbers mean:
1st number: Issued by the Finance department (1) or treasury (2)
2nd to last number: printing contractor
Last number: printing contractor's factory number
The numbers in between, in your case the 2nd, 3rd and 4th are the block/run numbers.
So yeah, these are not errors. The 1 yen, 5 yen, 10 yen and 100 yen (although it has an extra serial) from this series all have the same numbering scheme.