To clarify what I'm talking about, I'll give a list of cards which seem to go against the typical system without any obvious reason.
I literally just explained the system, but you still seem confused so i'll be clearer. Almost all of your problem cases were explained by my system. This is my last time I am looking at this thread so I don't get worked up. Its been a long day.
to recap:
A) Epics, uniques, legendaries, and/or equipment get (3). If they are also mage-only as well, they get (2).
B) Being mage only does not reduce the card count in and of itself
C) If not A, level 1 cards get 6 copies and level 2+ get 4 copies, so you can fill a spellbook with them.
D) The intent is that you can make any one spellbook from the resources (provided you never cast multiple epics, uniques, legendaries, equipment)
problem cases
the few you listed which actually do not follow the system if your information is correct:
Mana Prism x 4 (should be 3) UNIQUE
Otto Kronig, Master Engineer x 4 (should be 3 LEGENDARY;
-Combustion x 4 (should be 6; level 1;
-Skeelax, Taunting Imp x 3 (should be 2; warlock only AND LEGENDARY)
and some other cases if i remember correctly:
barracks should be 2 not 1
[mwcard=FWE09]Standard Bearer[/mwcard] (2 not 1)
there may be more, but I am not hunting them down tonight.
as for why these specific counts are off,
The system is determined by printing sheet sizes, most likely.
two or so card totals per set get rounded to make the right count for the sheets. Hope thats what you are looking for.