1) Does your H Bridge driver require the enable be temporarily off
when you put it into brake mode ?
2) You are observing the timing and ratings in the datasheet for brake
mode motor current....?
3) Use a R, say 100 ohms, in lieu of a motor and observe the timing
you get, that at no time in any vertical path in hbridge leg both output
on....shorting supply to ground.
4) You implemented the chip bypass recommendations in the datasheet ?
5) If external diodes part of the recommendation in datasheet you have those in place.
Regards, Dana.