When S1 and S4 open at the same time due to overlap in the gate driver signal (why they overlap is the real reason?), then the power shorts and you see the stored BEMF going back into the (-).
Zoom into the S1 and S4 gate driver signal going into the fets to see if there is any overlap.
You should see a clean PWM F4 driver signal but overlapping gate drive signals, i.e. they will be a little off-phase.
This is a guess.
Valentine