Normally the drone will climb to the set RTH height before returning home.
Negative height wouldn't make any difference.
The only thing that I'm aware of that could stop it climbing is mentioned on p 15 of the manual.
When the RTH altitude is set to more than 65 ft (20 m) and the aircraft is ascending between 65 ft (20 m) and the preset RTH altitude, the aircraft will stop ascending and immediately return to the Home Point if you push the throttle stick.
For that to have happened, the drone would have had to lose all signal, initiate failsafe RTH and then establish downlink enough for signal to the drone to work and for you to have pushed the throttle up of down.
It's a bit of a long shot, but all I can think of.
That would be a reasonable assumption.