I can´t obtain the same results in Fresnel coeficients of a materials with complex refraction index (bi-layer dielectric thin-film) with angular incidence.
Finite Element method is suitable for complex problems. If you have problem and used both methods to solve the problem, the answer should be same with small error. Further, You may have a complicated problem with no available analytical solution, Then you, must go to the finite elements methods. The question is how to validate your results ?. You need then to validate your FE results using experimental analytical results.