It should be impossible to get Cultivated by breeding a Noble with a Noble. Unless something has changed; Noble is a recessive gene. If you have a noble bee it must either be pure or mixed with another recessive species. Cultivated is dominate so a Noble and Cultivated hybrid will always be Cultivated-Noble. Never Noble-Cultivated.
Right?
I don't believe that's true at all.
What getting a cultivated out of what he thought was a noble/noble breeding pair tells me is that OP isn't doing it right. He should be doing three different steps with as much parallelism as possible.
1. Breeding pure bees for mutations. When trying for a mutation, ALWAYS breed pure bees. And by pure, that means the same species in both active and inactive side.
2. Combining hybrids to get pures. This is where you combine either two hybrids or a hybrid and a pure to try to get pure bees of the type you want. It is also good for separating the hybrids back to the pure form of the parent bees so you can do step 1 again with the same bee.
3. Replicating a bee by putting a random princess in the apiary with the pure drones of the species you want.
Here's where probability comes in. If you run 4 (or more) different apiaries with soulframes, you ought to get at least one pure mutated bee of the type you want, and a bunch of hybrids. Sure, each individual pairing might have a low chance, but when you do several at once, you'll have a much, much better shot. The only downside is that you need a massive line of replicators (or the extra bees machines) to keep making more princesses of the parent bee species. I find that oblivious frames works really well for gettting a nice stock of drones that you can them slap into automated apiaries and use as a low-tech form of replicator. Keep in mind, with this process, every time you are doing step one, you will need to make a fresh set of 4-6 princesses.
Sure, you might have bad luck and just get a bunch of pure drones in a row after Step 2, but then you just do Step 3, and you can convert any princess at all into that species. If you do it right, you will ALWAYS move from "pure trash" to "hybrid" to "pure treasure." Just make sure that you are analyzing both princess and drone so you never combine two hybrids when there is a pure drone available.