Nope, works as intended.

Hmm.... judging by

http://www.d20srd.org/srd/spellLists/clericDomains.htm ,

in d20, all domains have one spell at each level, so Neverwinter Nights isn't a good parallel.  Enforcing the one-domain-spell-per-spell-level rule in the nwn context encourages players to pick domains with non-overlapping spell slot levels which detracts from picking them in a manner suiting the style of the character (e.g. Magic/Evil to get two negative energy bursts for an evil cleric looking to buff his undead subordinates).

I'm not convinced this was what was intended.