Most likely the problem is related to a size mismatch between the x, y , z positions passed to the topology object, and the FDTD grid.
Ensure that the mesh override agrees with the x, y, z points that you have passed. Usually the mesh override should accomplish this, unless the mesh accuracy set in the FDTD object results in a mesh that is smaller then what is specified in the mesh override object. Maybe set a uniform in mesh in FDTD or reduce the mesh accuracy so that the mesh override does what it is supposed to. You can check the FDTD grid values in the simulation. Compare this with the points you have defined.