I know this isn't directed to me, but my sister and I also got separate by an airline after we had assigned seats (booked together and on the same confirmation number). The airline was United and it was in July of 2010. It was a short flight, and we are both adults so it wasn't too much of an issue, but it still irritated me. It was a flight from Chicago to Peoria and even though I had been checking periodically for changes, by the time I noticed there was a change, the flight was full and we were sitting a few rows apart. I called to see if we could be moved together, but they said since the flight was full I would have to ask at the counter. Since it was only a 45 minute flight and we had just gotten off of a long flight from Hawaii we didn't bother to ask to be moved.
Our assigned seats on the flight from Hawaii to Chicago had also been changed and they had us separated on that one too. Luckily that was a big enough plane and not sold out so they could move us back together for that flight.
So, yes, this can happen. Now I always check my flights multiple times to make sure our seats haven't been changed. Maybe it is just an issue with United.