From Bulbapedia, the community-driven Pokémon encyclopedia.

The berry glitch is a glitch in Pokémon Ruby and Sapphire which seems to freeze the growth of any berries which have been planted but not harvested. The glitch typically occurs after about a year or so of owning either game, and is alleged by some to be the trigger for the Celebi glitch. It also seems to happen to games that have been played over 100 hours.

Patching

The glitch can be fixed by downloading a patch from Pokémon FireRed, LeafGreen, or Emerald, or by sending the affected game to Nintendo.

1. Load FireRed, LeafGreen, or Emerald until the title screen is displayed.
2. Press the Select and B buttons. After the new screen loads, press A.
3. Insert the Link Cable so that the system that has FR/LG/E in it has the Player 1 cable port inserted and the one with R/S has the Player 2 port. Once this is done, press A.
4. Turn on the device with Ruby or Sapphire while holding the Start and Select buttons.
5. Refer to the FR/LG/E display for further instructions. The patch should be transferred at this time.

Although the glitch prevents berries from growing, it does have one upside: Pokérus is supposed to disappear after a certain amount of time, but this glitch prevents it from going away.

Also, there are a few other known ways to get the patch, such as linking to the GameCube Colosseum Bonus Disc that gives players Jirachi. If the game has not yet been patched, before Jirachi is sent, the disc will send the patch.