You can click on the dice you want to keep, you don't have to use the score options.
In order to maximise it's chances of rolling a high-scoring multiple the Realist CPU will only select one of the dice in a pair. You'll note that the score option doesn't "ping", that's because the CPU is clicking the dice instead of the score option.
I will make the CPU player ping the dice when it clicks them, to make it more obvious what's going on. This is not a bug, this is the CPU trying to be smart about how it plays. Please stop sending bug reports about it.