Disconnected winding phenomenon
Given that you're talking about windings in a (presumably running) motor there could be some magnetical field remaining giving EMF. When you disconnect a winding it's not actively pulled to a rail by the bridge leg so it has to dissipate somehow. A similar phenomenon (the rotor still turning) is actually used for sensorless switching, which it seems its the thing you want to do.
The thing I don't really get is the step at about t=780, which seems from another data line… what would be its meaning