Here's something that just happened without consequences other than a surprise, but that has some potential for a bigger scare or worse:
Aircraft: DJI 550 Hex w. APM 2.5 & 2.9.1b firmware, JR 12X Tx. Armed and took off in Stabilize but landed again right away to make a physical adjustment. Did not disarm but flipped on "throttle hold" on the TX (I have that set up to lock the throttle to zero on everything I fly to avoid a prop start if the throttle stick is accidentally bumped). Made the physical adjustment, flipped throttle hold off and attempted to take off. No response from throttle stick, just as though throttle hold was still on, or as if APM was disarmed. WTF? I had no idea but decided to disarm and so moved stick to lower left. Instead of disarming, three props immediately spooled up!! Discovered that while the throttle stick was completely dead, yaw, pitch and roll inputs would spool up various combinations of props. And they would do this regardless of whether "throttle hold" was engaged on the Tx or not. So had I bumped either stick while my fingers were in the arcs it could have been ugly.
What had happened is that after landing and while leaning in fiddling with things I apparently bumped the Tx mode switch from "Stabilize" to "Alt Hold". Once I figured it out I reproduced this behavior to verify this. I presume, but did not test, that something similar would happen if "Loiter" were engaged on the ground.
This behavior is not a really a bug, the controller is actually responding appropriately to commands. But it does make for cheap thrills in this situation. It would maybe be better if Mr. APM knew when the aircraft is planted on the ground and didn't try to make silly gymnastic moves.
The moral of the story: While you can't arm APM if it's not in Stabilize, you can get into a mode from Stabilize while on the ground that can result in unexpected prop starts. Double check your Tx switch positions before each flight and before sticking your fingers in harm's way.