Possible SHA-256 implementation weakness
Quoting zaph from the comments:


  If the implementation does not produce the correct results it is a failed implementation, don't use and report it. 


This is pretty much the correct course of action, assuming that the algorithm is supposed to be SHA-256. 

Cryptanalysis of the incorrectly implemented algorithm would be non-productive, unless your goal is to maliciously exploit the protocol that is using this hash function. 

Alternatively

It is possible that the author was attempting to be clever or obscure and made such a modification intentionally. There may not be much you will be able to do to help the situation if that is the case; Even if you present collisions/preimages, you may simply garner hostility from the author/users (see the drama around IOTA for an example).