I have had this issue myself a couple of times from 2-3 and have found a way of recreating the problem and also avoiding it.
For me at least, it seems that to make it do this, all I have to do is floor it from standing, tnen just as I get to the top end of the rev range in second, slightly lift off to "balance" the rpm and stop accelerating. What I have found is that this confuses the gearbox ECU (bad program logic), making it hold the gear for 2-3 seconds allowing torque to build up. Once the gearbox ECU realises it should change gear, there is a stack of torque waiting to be used and the net result is it all gets dumped into the gearbox as you change to 3rd + the RPM's get dropped really low, so you get a bang/thud and what I can only assume is a very bad thing for the clutches / torque converter!!
The ways I have found to avoid this is simple.
Option 1) if you floor it from a standing start or junction, be prepared to keep it floored well into 3rd, or else just don't floor it! 1/2 or 3/4 depression of the loud pedal wont create this problem.
Option 2) If you manage to catch the RPM sat high in 2nd as you have been accelerating hard from standing, but now need to slow down, don't slowly reduce the pedal angle, but instead, take your foot off the accelerator completely. This seems to tell the gearbox ECU to not change gear and lets the revs fall back down normally avoiding the torque being dumped into the box.
Option 3) use "sport mode" all the time. I find sport mode less eager to change gear at high RPM, and this can reduce the gearbox's likelihood to cause the issue.
From the research I have done into the issue and the gearbox in general looking for potential upgrade options to handle more torque, the general consensus is that the box is fairly good (its a Toyota ASIN TF-60 which is used on loads of different cars, rated up to 500Nm of torque). What's not so good is the logic in the gearbox ECU, which is designed by each manufacturer to suit the dynamics of the car/driving style etc.
That said, in fairness to the car and its programming, mine only does this when I decide to be a bit of a boy racer and floor it from junctions, then remember I am a grown man and am in a built up area and back off the accelerator at the speed limit
If I accelerate from standing to 100+ (on a track of course officer) The gearbox is silky smooth and just perfect.