There's no explicit contradiction there. The movie makes it clear that no single Torp Bay is connected to a specific torpedo tube; that is, Torp Bay 2 feeds both port and starboard tubes. Thus, there is no onscreen reason to think that the number of Torp Bays and the number of torpedo tubes would be related in any specific way.
If the ship has more than the two visible torpedo tubes, though, then one must wonder why these would be both invisible
I mean, in TOS, all
torpedo tubes were invisible - but here two of the lot very clearly are not! Why would there be inequality in visibility? Why should some tubes deserve cover plates when these two do not?
Or are we speaking of weapons of differing calibers, perhaps? The ship does have visible features suited for firing smaller torpedoes - say, the four indentations on the back of the secondary hull, never seen doing anything much (the designer apparently intended these to be thrusters or vents of some sort, but no such thing was established on screen).
OTOH, TOS only ever showed torpedoes being fired forward, even though ENT showed that a ship nearly identical to Kirk's had aft tubes as well. If Kirk in TOS occasionally decided not to use his most advantageous weapons (e.g. in firing the over-the-shoulder shot in "The Changeling" from a bow tube), certainly he has the right to refrain from using his hidden tubes in the movies as well.