Amazing: it is inconceivable that a dose of clean lubricant of the same grade as the dirty stuff removed would wreck a tranny. I agree with you: something had to happen with pressures or flow rates in the flush machine to cause this to occur. These machines run the fluid through the cooler lines, hence through the valve body and pump, so any excess pressure might blow a seal or weak element.

The real lesson is to keep the fluid clean to begin from the time the car is relatively new by regular draining and occasional flushes. And the flush should be done manually as noted in the FAQ, refilling through the fill tube.
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See the 700/900 "FAQ" at the menu bar top screen left side.