What could it be?
To prevent piracy, Nintendo implemented an infrared communicator within these cartridges which isn't found in ordinary cartridges. The game will check the status of the infrared communicator at certain points in the game, if there was no response from the communicator
The game would assume that it's either pirated or is being run on an emulator as illegal copies don't have this infrared communicator. If the game believes that this is an illegal copy, the players Pokemon will stop gaining experience which limits the progression of the game.
This feature is there to discourage people from playing the game illegally.