It is correct result, as now you are simulating a waveguide that confines the mode in a very small area. This is different from the traditional, textbook weak waveguide which has neglegible longitudinal field components. Acutally now the mode is hybride, not the conventional transveral mode that can have only Ex and(or) Ey.
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New Post - Reply To: FDE mode solver (2d-z ), E field is dominant to the Ez ( weak on Ex and Ey)