first guess is your rapid is to high and it dumped a shitload of steps moving to zero at whatever rapid you have set up at ready for its 3rd pass, however, looking at the photo it looks to have lost steps equally in two axis so it may well be something a tad more elusive

maybe the draw on your power supply is getting close to its limit with two axis at full speed?

if you have set your rapid speeds by pushing one axis at a time to its limit then backing off this problem would have stayed under the radar
its worth having your machine zig and zag at full belt then see if it returns to zero