I've gotten "There's been a change in your flight, please click to confirm" message on my Delta Iphone app -- when it looks like I'm flying towards a missed connection. I usually ignore it no ill effects -- either I run and make my "impossible" connection, or I go to the Skyclub or departing gate to check-in for the next flight. It seems like the system is double-booking me on the original and the next logical flight.

You mean to say that's not the way it usually works?