there are many reasons to have this warning. this warning appears when the diagonals of stiffness matrix corresponding to one or more dgrees of freedom is zero. this can be due to
1- using of shell element in representing plate structure, due to zero diagonal term corespoding to the rotation about the axis normal to the plate.
2- missing boundary conditions at any node.
3- there is a node which is not connected to elements
4- could be other reasons which can be known after check your model