pert:
The biggest problem I've had with crimping the Dupont style connectors is using too much force. Once I learned to stop as soon as I hear the ratchet on the crimp tool disengage I've had excellent success rate. The other thing that was causing me a lot of problems is when I'm doing a cable with a lot of wires the ones in the middle would have slack and the ones on the outside would be taut. I had to get a feel for how to cut each one at a different length so that they all end up even once inserted in the housing.I still greatly prefer using the IDC connectors because they're so much faster but sometimes there's no choice but to use the Dupont style connectors.
The ratchet tools are all adjustable. You should adjust it so that it doesn't over-crimp. The reason for using those tools instead of pliers is they make it impossible to over- OR under-crimp the connectors when adjusted correctly.