I think maybe someone was in the process of working on the roof and moved the stones out of the way and piled them up by the chimney. See the darker area of the membrane in the bottom left corner of the pic? That looks deteriorated to me. If you zoom in, you can see the alligator cracking there. It is either a different age than the rest of the roof or deteriorated quicker there. Possibly ponds water in that area, which increases the rate of deterioration.
You can also see roller marks from where they applied a roof coating of some type over the membrane. (to the right of the darker area at the bottom, 3 roller marks right next to each other.)
The stones are functional like Tony explained and they also help to block UV from damaging the roof.
cnystul1 you definitely should recommend further evaluation by a licensed roofer for this. I would bet that roof is well past it’s life expectancy and has been coated at least one time, maybe more.