Thank you all in advance for any insight!

The first photo shows our newly installed thermal bluestone patio about a month ago (sprinkled with some buds from the overhanging maple tree), and the second photo shows some of the patio after a heavy rainstorm a few weeks later. Although the installers state that they have never seen this occur and used their trusted supplier, they are trying to blame the maple tree, which we agree is likely the source of the brownish-orange cast (which can be removed with vinegar), but I cannot find an instance or figure a reason for water running through the tree to have created the black smudges and splotches and the deep discolorations of certain stones. We did not spill anything on the patio after it was installed. Does anyone know what may have happened here? A substandard batch of stone that maybe should have been sealed?

Thank you!