For example, creature cards have power and toughness. Simple enough. But then at some point, cards were printed that allowed you to modify those values. Now you have to mentally keep track of the actual state of the card. Then consider what happens when you have two effects like "add two to toughness" and "switch power and toughness" applied at the same time. Which one happens first? Much as in software, each new feature of the game inevitably has interactions with other features that have to be analyzed and handled appropriately.
Going back to the main point, this complexity is 'artificial' because it is not an emergent property of the rules themselves, but rather a consequence of the fact that so many rules have been piled on over time.
(Also, that a creature's power and toughness might change has been part of the game since the very beginning: see Giant Growth.)
Concrete example: castling[0] in chess