I've noticed the same Korea bug. I understand why it's there in the beginning (so that the Soviets have a chance of breaking through and capturing Korea) but once you have vacated Korea it should go away but it isn't. It's a really big pain in the butt if you try to retake Korea as the Japanese and that is when it should definitely be removed.
One other bug that I've noticed in the Pact of Steel scenario is that the Soviet AI is receiving artillery pieces even though I have the no artillery default settings in place. I am 100% positive I have this setting in place too. No other nation has artillery or even the option to research or purchase artillery.
A third possible bug is that the Axis AI fails to defend Prokopyevsk (near Novosibirsk) if the Chinese break through in the west (above the Himalayas).
I'm pretty sure this is a bug but Prokopyevsk also has zero supply even without me taking the city over (that may be preventing the Axis AI from defending it.
Other than these small bugs and some of the minor script bugs that you mentioned and that I've seen as well, there is nothing wrong with the scenario. It's actually pretty darn awesome and the AI is performing very excellent (especially the German Naval AI).
I'm playing on intermediate/+1 experience and getting a very good run for my money as Allies. That Axis air power is devastating and I am really paying for my ineptitude in not researching naval as the British.
