I posted something about this a long time ago, when I noticed the same thing. There are two Berry glitches to look out for. First is the notorious "clock-berry glitch", where the berries stop growing after a certain number of hours played, and this can be fixed by linking up to Fire Red/Leaf Green, or XD, or whatever.
The second one really isn't a glitch, but it's useful to know about. I coined it the "Brownian Berry Glitch", because I pioneered the questions, and in science you're allowed to name a discovery after yourself. ;)
And basically, what the above said is correct. If you do not pick berries for a while, they completely disappear. I did a few tests, and watering berries makes them last longer, but you must make sure you pick them as soon as possible. It happens in D/P too, and the berries that grow faster can disappear in as little as three days if you don't touch them. Some can be faster, but like I said, in my tests I noticed that berries you water last longer than berries you don't water. But you still should pick them as soon as possible, to avoid having them just die off.
Hope this helps a little bit!