A bug that is entirely inconsequential except for the very very specific case of a user exploiting it deliberately on their own device to run Bannerbomb3. This is a pointless distinction, the tech equivalent of "I'm not punching you, I am just holding my fist up and running in your direction with my eyes closed and if you get hit it's your fault!"
"Bannerbomb3" is referring to an exploit in their system settings which allowed for custom firmware to be installed on the device. So fixing the bug which allowed the exploit is what is considered to have "blocked Bannerbomb3".
Personally, I think it's rather likely that Nintendo did this specifically to prevent their customers from installing custom firmware on devices they purchased, rather than because Nintendo wanted to fix a bug for any sort of perfectionist or altruistic ("user security") reasons. It can just be dressed up as a security issue, so that's what they do if they feel the need to justify it at all.