Using $5.2 mathrm{fb}^{-1}$ $e^+ e^-$ annihilation data samples collected with the BESIII detector, we measure the cross sections of $e^+e^- to K_S^0 K^pm pi^mp pi^0$ and $K_{S}^{0}K^{pm}pi^{mp}eta$ at center-of-mass energies from $3.90$ to $4.60$ GeV. In addition, we search for the charmonium-like resonance $Y(4260)$ decays into $K_{S}^{0}K^{pm}pi^{mp}pi^0$ and $K_{S}^{0}K^{pm}pi^{mp}eta$, and $Z_c^{0,pm}(3900)$ decays into $K_{S}^{0}K^{pm}pi^{mp,0}$ and $K_{S}^{0}K^{pm}eta$. Corresponding upper limits are provided since no clear signal is observed.