I have noticed this problem.
As explained in the intro notes, the index was prepared form the LDS catalogue which itself is available on two microfilms (Arch & Epis).

The only way to make an accurate index is to inspect each film. I have neither the financial nor time resources to undertake that project, but if anyone comes across instances I will be pleased to up date the index.

I am trying to cross reference MNH and LDS film numbers.

After several years using LDS films, I noticed on the last film I ordered a hand written number at the beginging of the film which appears to correspond to an MNH number. Maybe I've been missing something. Live and Learn.