Hello commander,
I'm afraid you are correct as in that there is little we can do for compensation here, since this is not really a bug. If you open the supply window your currently selected-as-active base is chosen as destination. You can change the target base with the dropdown list in the supply window, in the upper right part of the supply window.
However if you use your base shortlist on the right side of the screen, the supply window updates the target destination. This has been intentional from what I understand. I can see however that this redundancy may cause some confusion or errors for players in your case.
Sorry for your inconvenience in this matter. The only thing i can is to see if we can remove the redundancy so players don't designate the wrong base by accident, in the future.