A theoretical investigation of spin wave dynamics and scattering at a molecular junction between two Heisenberg ferromagnets is presented. The model system consists of two ferromagnetic ultrathin films with equal thickness of three atomic layers, joined together by a magnetic molecule. No electronic effects are considered, but local changes in the magnetic exchange field are assumed to be dominant. The mathematical framework of the matching method is used with nearest neighbor magnetic exchange interactions, to analyze both the spin fluctuation dynamics and the spin wave scattering phenomena at the junction boundary. The coherent reflection and transmission probabilities and the conductance of spin waves incident from the interior of the films onto the boundary are calculated in accordance with the Landauer-Büttiker formalism, and numerical results are presented for representative sets of system parameters for a large range of scattering frequencies. The scattered spectra show interesting sharp features, with associated Fano resonances, as a function of scattering frequencies, system parameters, and spin wave incidence angle. Moreover, a frequency selective conductance of the spin waves via Fano resonances can be obtained by an appropriate choice of the spin wave incident angle and system parameters.