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.