The Charlton Catalogue uses the mintage figures provided by the
RCM. If you look at the numbers the
RCM listed in its 2012 and 2013 Annual Reports for the two products you've mentioned you'll find that they match what is in Charlton.
It is certainly possible that the 1,499 mintage for the five-ounce coin is a matter of a coin being damaged such that it could not be sold and it was not subsequently replaced with a fresh strike. If you look at the mintage figures for each of the coins that the
RCM has listed as "Sold Out," you will find that almost all come close to the stated maximum mintage figure but do not reach it exactly - it's almost always a case of damaged coins that were either returned or detected internally and not replaced with additional strikes.
The extra set listed for the five-coin set is a bit more problematic as the
RCM should never release more than its published maximum mintage.
Of course, it might simply be a case of someone accidentally mis-categorizing a "five-ounce coin" as a "five coin set" and it not being caught before the figures were published in the pertinent Annual Reports.
In either case, being one coin or set off does not have any impact on the value the market assigns to either.