By Raman spectroscopy we investigate the substitutional disorder in (001) Zn1-xBexSe/GaAs epitaxial layers with low Be-content (x less than or equal to 0.30). We demonstrate that the asymmetric broadening of the ZnSe-like longitudinal optical mode (LOZn-Se) is determined by topological disorder and not by other possible mechanism such as structural disorder, non-homogeneity in the alloy composition, distribution of tensile strain or Fano-type interference. This reveals that Zn1-xBexSe can be grown of high structural quality. For allowed phonons topological disorder results basically in the breaking of the translational symmetry, which leads to the contribution of q not equal 0 phonons to Raman scattering. Quantitative information upon latter finite-size effects is obtained via a spatial correlation model with Gaussian distribution to describe the relation between disorder and the lineshape of the allowed LOZn-Se phonon.