Why do so many of my cities have a science output of zero?

Why does Ayr, a city with 358 Commerce, have only 40 Science, when Mount Isa, a city with 306 Commerce, has 210 Science? (Ayr and Mount Isa have the same building inventory, so their total building maintenance is identical.)

Why does Cairns, a city with 8 Commerce, have the same Science output as Alice Springs, a city with 194 Commerce?

For that matter, why does Cairns have only 8 Commerce? It's a size 20 city, and within its city radius are 7 Forest tiles (10 Commerce each) and 4 Beach tiles (10 Commerce each). Similarly, Ultima, which is listed as having only 3 Commerce, has 6 Forest tiles and 6 Beach tiles within its city radius.

Is this a bug? Or is it some inexplicable part of the game design?

I've seen exactly the same thing in my game!
I think it's some kind of bug in the game. Total Science appears to be accounted for, however. I also noticed that I usually have one city producing a disproportionate amount of science compared to the other cities.

I hope someone can provide an answer...