It's a revolving door system. They don't actually care what's wrong with your console, if you bring something in to be fixed and pay the "repair fee", they crudely toss the broken unit into a plastic "incoming" bin and hand you an entirely different console from their "outgoing" shelf, in order to rush you out of the building quicker (because they hate your face respect your time). If you go in with something to be fixed on one of the first days of the console, you're probably going to handed a brand new system after paying the "repair fee", not getting a repaired one, because there are no "repaired" units for them to give you, and they're not going to have you sit around and wait while the unit gets fixed (not even for something as simple as a battery replacement).
As their repair guys have time, they dig through the "incoming" bin full of broken consoles, and fix whatever they can fix. When something gets fixed and tested, it gets a good cleaning, and then Nintendo declares it "good as new" and puts it on the "outgoing" shelf, so that they don't have to keep putting brand new consoles out there.
Some guy got his console banned, so brought it in to Nintendo to be "repaired" (while deliberately leaving out the part where he got his console banned), and the repair guys fixed the obvious broken part while neglecting to look at the software and didn't realize that the console was banned.
Nintendo is shocked, shocked, I tell you, that one of their repair guys skipped the step of hooking the console up to a machine and testing it's software to see if it was banned or not. That's supposed to be a part of the repair/testing procedure! So Nintendo spent a week, two weeks, three weeks, a month, doing an investigation into their repair people, while leaving their customer sitting on the doorstep saying "Hello?" instead of giving the customer another "good as new" unit from the outgoing pile, to fix an issue that Nintendo was to blame for.
And to think, all it takes to get basic customer service these days is to get the support of 45,000 people on social media.