The game tells you about this problem and how it expects you to get around it in the story, even giving a lore explanation in that mental link is janky. so I figure it's intentional. That, or they just couldn't fix it in time and made a joke about it in the story.
I believe the gameplay loop is meant to be, click near the thing you want to interact with, switch characters and give them an order, then tell them to move to the next thing before switching back to have the first one interact with their thing, tell them to move somewhere, repeat.
A bit more involved than necessary, but feels good when you get the hang of the flow. I do think I'd prefer if it were simpler though.