I use a punch anytime I can. I haven't had any issues with my 9mm Xikar as of yet. I do tend to wet the cap with my tongue then apply a small amount of downward force while rotating the cutter. I haven't had any issues yet with this method. I have mine stored at 65rh using Bovedas so they are kind of in the middle of the rh spectrum.
It might have to do with using the lighter built in punch though. I tried that in the beginning and had the same split caps as you. It's hard to get the force square with them. I always felt like the lighter was in the way. I went to the seperate cutter unit and all problems went away. Plus, I got to add another toy to mess with.