When you say you're formatting - what exactly are you doing? Are you actually trying to format a floppy? Or do you mean that when you've installed and booted into WB you find these rogue disk icons?
If it's the latter, then it's probably a hardware problem.
Have a look inside the Amiga and check out the floppy cable. Make sure it's connnected properly and is a standard Amiga jobby (i.e. no twisted conductors. Also check the drive to see if it's an original Amiga item.
The problem (I think) stems from the select lines being driven low making the OS think that you have DF2 and DF3 connected to the internal floppy header (or external floppy port). As far as I've been able to ascertain, the select lines shouldn't be physically connected.
It could just be that the custom chips that control the floppy drives have gone 'bad' - in which case a new mobo would be required.