The limitations of CARINA are many - I would have had probably 10 trips in recent years that have all had similar issues where some (but not all) partner flights can't be confirmed at the time of booking. The error messages generated are pathetic but there are no resources being put into fixing some of these limitations because they occur across a very small percentage of the total flights booked. It is also worth noting though that not all issues where this occurs are because of CARINA, some are because of GDS limitations of some 3rd party carriers.
Having said all of that there are many that believe CARINA is still one of the biggest advantages Air NZ has. Their ability to customise their core booking system exactly how they want has given them the ability to bring products to market quickly such as S2S which would not have been possible at the time with other GDS platforms, and likewise their dynamic pricing which they're about to trial this year is also not possible in traditional GDS systems.