as said above brown pathces is iron ore in the slate, a good test if you're using low quality slate is to drop a drop of vinegar onto the slate or patches if it bubbles dont use it.
I build my own caves from slate, I tend to use slate which has been crafted for floors, its thick and pretty strong, and also tends to be pure slate (if thats even possible, seeing how slate is produced, lol)
You may find roofing slates to be a bit thin and when you are cutting them to size they may shatter, but it depends.