Various reasons, but generally if it's not obvious it's because the good ones were already taken, rather like .com domain names e.g. Abuja was only built relatively recently in aviation terms and ABV was probably the closest unused code IATA could find,

EZE is an airport code for the city of BUE. This generally happens when somewhere has (or had) more than one airport,

But I'd love to know the story behind the Yxx Canadian codes. Anyone ?