Two problems

So this is my first real grow, and I think I might have run in to an issue :/. So the first issue is I have rooted my clones into 6" rockwool cubes, and without growing more than an inch in height they have already rooted through to the bottom of the cubes, and I have nowhere for the roots to go! I was expecting them to break through the bottom once they were ready to be transferred to my aeroponic system but it seems they are a little over eager, what should I do? They still have at least 2 feet to grow before I even consider transferring them but the roots are hauling ass outta there. The other issue is the smaller cubes I transferred into the big guys are turning black on top, is this something I need to worry about? Thanks for the help in advance.