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We investigate how magnetic impurities may affect a system exhibiting charge-density wave (CDW) in its ground state. We consider a disordered Hubbard-Holstein model with a homogeneous electron-phonon interaction, but with a (randomly chosen) fraction of sites displaying a non-zero Coulomb repulsion, $U$, and perform state-of-the-art finite-temperature quantum Monte Carlo simulations. For a single magnetic impurity, charge-charge correlations hamper the spin-spin ones around the repulsive site, thus requiring a strong enough value of $U$ to create non-negligible antiferromagnetic (AFM) correlations. As the number of magnetic impurities increases, these AFM correlations become deleterious to CDW order and its features. First, the critical temperature is drastically reduced, and seems to vanish around 40$\%$ of impurities (for fixed $U/λ=2$), which we correlate with the classical percolation threshold. We also notice that just a small amount of disorder suffices to create a \textit{bad insulating} state, with the suppression of both Peierls and spin gaps, even within the charge-ordered phase. Finally, we have also found that pairing correlations are enhanced at large doping, driven by the competition between CDW and AFM tendencies.