I am sculpting a mesh and joined the head to the body with a boolean modifier and every time I join any meshes together they form these edges that I can't sculpt away. Both meshes have had all modifiers applied and the only difference is that the head was not sculpted and contained a different number of vertices from where I joined it to the body.
Umm I dont know if you already solve this, but I Have those kind of problems when I use zbrush usually is because your object wasnt dynamesh prior to merging, and you only merge them together in their plain sculpt mode so you are not adding geo to the object but intersecting the geometry of both meshes, also boolean is horrible because you get ngons everywhere, thats why some geometry can collapse on itself like is doing in your picture. Probably blender works similar to the dynamesh in zbrush.
Are you sure that all vertices and edges match fine? Try removing doubles and apply rotation and scale to that mesh, also if you could share that topology so I can see if there is another kind of issue