After more extensive play, as both Germany and Japan and USA(Pacific), I wanted to add some more observations:
1) I too noticed the "invincible air unit" anomalie, but it was in a fort not a city and I was trying to take it with infantry or tanks. Hopefully this has been fixed as you say, but wanted to point out it wasn't limited to cities.
2) Perhaps for the noble or lower levels, at least put a remedial militia type unit on the unoccupied islands in the Pacific. It takes 200 some turns to build anything out there, so I was easily able to sweep in and clean up those islands basically for the price of loading a transport. So far on prince level I am noticing that most islands have garrisons so maybe it is a level issue. Again, a half-strength type unit might be enough.
3) Colonies. I notice oil in Alaska, and I build a fort (connected by rail) there but it doesn't grab the resource nor will it allow a well since of course it is not inside my borders. Perhaps this isn't how it is supposed to work? Perhaps adding a couple settlers at the start of the scenario (but without the ability to build any more) would help?