In short, the patch was designed to target allied NPCs in missions who didn't attack, but buffed the player characters to the gills in order to make missions easier. Unfortunately, caught in the crossfire were almost any missions that involved things other than enemies, up to and including missions where players would rescue hostages. Needless to say, player response has not been kind.
Sean "Dr. Aeon" McCann was quick to give an official statement on the matter, explaining that the idea was to implement a temporary fix that would prevent current farming, with a more permanent one coming around Issue 17's launch. (Although we don't have a specific date on that, it's been generally pegged for early this month.) Until then, City of Heroes players might find themselves advised to take a break from Mission Architect for a little while.
[ Thanks to Steve for the tip! ]