Banktivity icon shows three folders

Try this.

Go into Banktivity and on the top menu bar click File/Open Recents/Clear Menu.

This won't delete any files but it should clear the list of recent files that I think is what you're seeing on the Banktivity icon. If this doesn't fix it then I don't know what's happening and you'd be best raising a ticket with Banktivity. They are pretty responsive in my experience.

What do you mean by "the icon lists three folders"?

I just click on the icon and the app opens the last database that I was using. What exactly are you doing?

Have you tried using Finder to navigate to the folder where your Banktivity file is and just double-clicking that file?

You're welcome.