Cloning: Rockwool sitting on Perlite

I am cloning with rockwool and Clonex and I put like 30 clones on Perlite and closed the lid for a couple weeks. I came back and the majority of the perlite below the rocwool was green and slimy and the rockwool was hit hard with it. All the plants rooted with decent looking white but small roots, however the plants (leaves, stem) kinda looks like shit.

Should perlite only be added after the roots show, to not precipitate the green slime / mold in the first week or two... Or is it fine to add perlite when cloning in humidity domes with rockwool, it was just too moist or my environment was too hot or cold or something??

Thank you!

Why was the perlite being used at all? It sounds like damping off.

I put it in to make it look nicer. It was for an order so I wanted it to look as nice as possible. Also, I figured it would make the plants healthier by giving them something to root into rather than just the rockwool.

So I looked up Damping off and maybe its that. It was very wet in the humidity dome(on the too-cold side in my clone room) so maybe adding a heat pad would dissipate more of the free standing water and make it less damp / more humidity?