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Currently you can raise population to 13 times the planetary size. So with a size 9 world you can have a max of 13*9 = 117 POP on the planet. Without an Ag center you can increase POP 1 per action per turn. With an Ag Center installed you use the exact same command of increasing by 1 and instead of 1 your POP increases by two. However... Say you have 116 POP on a size 9 world and you want to max the POP out, and you have an Ag Center installed. You put in the same command to increase the POP by 1 and... fail! Unable to increase POP. You are left with 116 of 117 POP on the planet and a failed build action. Hopefully this will be resolved at some point in time but in the mean time you can pull off 1 POP so your build action will increase 2 POP up to the max.

I don't remember that happening to me.

as i understand it you are doing ac3 planetXYZ12311 qty1bcde261.
i know the rules says that if you have an ag. center it will build 2,

two pop units are automatically built, even if only one is ordered to be built.

I have always just ordered two built and have successfully built what could be built.

This is what happens when I work off my to do list. I had tested it a year or so ago and was getting failures. Now it works correctly. My bad