When you open the ballvalves, generally you recirculate the wort/runnings back into the MLT until they run clear and without debris. I wonder if you didn't do that, if you have some grain debris in the kettles. If it's not grain debris, it is probably break material, and that is totally normal. Coagulated proteins clump together and fall out, and that's a good thing meaning clearer beer in the end. That can go into the fermenter, as it won't hurt anything, so you can strain it out if you want but often it goes right through a strainer anyway.