Only simple flaps can be flaperons. Fowler and double-slotted flaps generally used on large aircraft cannot move upward, and are designed to extend slowly, which is more appropriate for their complexity and fairly large effect. But that's opposite of what you need in aileron, which must react quickly and using bigger deflection up than down is desirable to reduce the adverse yaw.
Normally in large aircraft roll control is augmented by using spoilers. These have the advantage that they create proverse rather than adverse yaw (the spoiler is raised on the inside wing and adds drag there) and don't suffer reversal at high speed as they don't torsion the wing. B777 is somewhat unusual in having a flaperon at all.
There have been air disasters where the airplane rolled uncontrollably for one reason or the other.
I can't remember any other reason than impeding stall, and in impeding stall the ailerons are reversed because deflecting the aileron pushes the wing deeper into stall and makes it go down rather than up. In impeding stall, the appropriate way to keep wings level is using rudder and yaw-roll coupling, which the pilots know.
Oh, and then I remember the Embraer E190 incident at Alverca (i.e. they managed to get it under control and land safely) where the control cables were connected crossed during maintenance, but in that case they were saved by the ailerons not having that much authority and roll control also employing spoilers which were still connected correctly and cancelled the ailerons at larger deflection.