There is a discount given in the form of a rebate when you are paying for the cost of field skills during stage 3. And the cost for field skills (because the number of skills varies per field) is not included in the life modules for that stage. So those have to be accounted for on their own.
Other than that one exception, for ALL the modules things should add up. I've found a few math errors, and suspect others have as well, so do check for Errata, especially if you have an older PDF. MOST of the stuff we found (other than some errors I noticed recently in one of the merchant modules for stage 4) got corrected in the printed book, and the most recent PDF which should be the same as the book.