The "problem" is that clicking chooses whatever bean is currently selected. You need to press A/D left/right to select the bean first, then click (or press enter). I'd highly recommend the dev change that, since I had this happen a dozen times until I figured out why I wasn't getting the bean I clicked on.
Thank you for explaining this... it is most frustrating that there is so little feedback from the input system that you can't tell what is happening!
Though it seems that there is also the problem of lack of responsiveness... sometimes it takes ages for the game to respond to input (space / enter) and sometimes not, this on top of an "auto-continue" that moves you on if you don't press anything sometimes applying... meaning you can end up clicking through the bean selection screen when you just pressed enter / space slower than the auto-continue but only just meaning you get whatever was already selected...
Interesting game idea but the UI is erm... needing a few more beans than Jack is capable of...