I score lines in brownies while they’re still warm from the oven and in the pan to get them sharp – once they cool, if you have the desired crinkle top, it is more likely to crumble when a knife goes in, which are the cracks I think you’re describing in the chocolate layer.
I’ve also been lightly buttering the knife or, of late, my Oxo turner if I’m giving them away, for clean lines with no crumbs / stickiness. (Sounds fussy, but works better for neat pieces than the previous method of chilling them before cutting – recent pic here.)
