It should detect that it is in the air, but you must have sort of tricked it into disarming by switching flight modes quickly or something. Maybe you should post a log of the flight.
I had a similar thing happen to me a couple years ago... I was testing a copter that was having compass/GPS issues so was often trying to fly off in a random direction. So, I was hovering it, seeing if I had good loiter performance, and it started shooting up into the air. In that split second I didn't realize what was happening and flipped the motor stop switch to stop what I thought was a random fly-away, and forcefully bring it down. (I realize now, motor stop wasn't the best choice in that situation, but I was a beginner)
Then I looked at the logs and realized it was just a battery failsafe...
Mine was the opposite of yours.. Electronics OK, but my frame was a complete loss, so I had to rebuild it.