The significant distinction in the module values between epoxy matrix and glass fiber could be the reason for such a big difference between FEM and analytical method in the values of the transversal properties.
Yes. it is the reason because the transverse properties are dependent of matrix as well as the reinforcement (for small amount). But we can't say in what manner the transverse properties will get change without having the look on constituents. We have to consider the amount of fiber and matrix being there, the properties of fiber and the matrix in the material to describe the nature and magnitude of the difference.
It is too vague to talk generally just FEM or analytical methods. For your microstructure, some analytical methods could be accurate such as Mori-Tanaka method, some FEM methods could be not accurate depending how to set up the FEM model, particularly the boundary conditions. You might want to try the general purpose multiscale constitutive modeling code at https://cdmhub.org/resources/scstandard
I have used E-glass fiber as a fiber and Epoxy resin as matrix material. Also, I took 50.24% fiber volume fraction to evaluate the transverse properties of composite. I found i my research that, In analytical method as Rule of Mixture the transverse elasticity is 6.58902678 GPa and by ANSYS 19.1 fem tool i got transverse elasticity 10.077 GPa. As fiber volume fraction increase, the difference in the result of ROM and FEM increases. Moreover, minor Poisson's ration give some strange relation between ROM and FEM.
If we are considering longitudinal elasticity, the result of ROM and FEM are same.