Please let me state up front that I am not a pathologist. However, I got out my Diseases of Trees and Shrubs by Sinclair and I would suspect...
Crown Gall caused by Agrobacterium tumefaciens, a soil-inhabiting bacterium.
Generally, it seems to be that the tree can co-exist with this unless it gets too severe or another pathogen takes advantage of the weakened state. It appears that the bacteria in the soil or water or on implements infect fresh wounds of any sort. Suitable wounds arise during propagation, transplanting, cultivation, frost heaving of soil or feeding by soil insects or nematodes... (This info taken from above book.)
So I would say that yes, the planting scenario (sharp rocks with frost heaving on young plant bark) certainly could have exacerbated a potential problem. (If this is in fact, crown gall.)
Sylvia