Manuals have always had these kinds of errors. Every IE game came with an errata text file(And pretty much every game ever), the BG1 manual described game mechanics that didn't exist in the game, etc. It's a little more excessive in this case, as changes have been substantial and ongoing, but
Regardless, it was unavoidable that the physical manuals would become obsolete. Just the balancing patches alone would make the manual incorrect on day 1, regardless of whether it was 100% correct for the release version. Same thing applies to the IE games, as well. This is just one of the many reasons why manuals aren't made anymore.
The digital manual will probably see updates, though.