I've been casually trying to determine any pattern in the eligible spend discrepancies and while still pretty random, I've noticed a couple of things.

First is that the folio you are presented with on checkout is often NOT what will be reflected as the final in the system (from a points perspective). So if you think (reasonably) you're good after you check your bill on checkout, think again because the eligible spend often changes if any adjustments have been made.

Second, if you're Diamond and take advantage of the breakfast benefit in the restaurant or room service, then there is a better than even chance there will be a billing issue on checkout. Typically any breakfast charges will be removed no questions asked on checkout, but know that this will almost always affect your eligible spend and thus, points accumulation. It's usually not enough to bother making a call over (<100) but shows how off their IT is.