I'm fairly certain this is the reason, but I would love to be proven wrong. Nintendo collects a ton of telemetry and probably has a way of detecting which cartridge is being played when. If the cloned one and the official one (or two cloned copies) is being played at the same time, you get hammered with a console ban. Simple as.
This is why MIG killed the second-hand market. You'll never know if your cartridge is being used by someone across the world. Thankfully, the people who use MIG are fairly rare in my country. But again, you never know.