That message comes from the bulk data constructor in Object3d:
public Object3D(float[] coordinates, float[] uvs, int[] indices, int textureId)
What it basically means it that the coordinates array has room for more triangles than the indices array actually addresses. An example: The coordinates array has 3000 entries, i.e. room for 1000 individual triangles, but the indices array only contains indices for 100 triangles. In that case, you would get this warning, because much room in the coordinates array will be left unused. jPCT can't re-index and compact that data, so it uses a coordinate array which might be much too large for the geometry. The message should make you aware of this. If you can change it somehow, fine. If not...maybe that's not an issue either. How many polygons does your object have?