Anomalies in the flux-ratios of the images of quadruply-lensed quasars have been used to constrain the nature of dark matter. Assuming these lensing perturbations are caused by dark matter haloes, it is possible to constrain the mass of a hypothetical Warm Dark Matter (WDM) particle to be $m_chi > 5.2$ keV. However, the assumption that perturbations are only caused by DM haloes might not be correct as other structures, such as filaments and pancakes, exist and make up a significant fraction of the mass in the universe, ranging between 5$%$ -- 50$%$ depending on the dark matter model. Using novel fragmentation-free simulations of 1 and 3keV WDM cosmologies we study these non-halo structures and estimate their impact on flux-ratio observations. We find that these structures display sharp density gradients with short correlation lengths, and can contribute more to the lensing signal than all haloes up to the half-mode mass combined, thus reducing the differences expected among WDM models. We estimate that this becomes especially important for any flux-ratio based constraint sensitive to haloes of mass $M sim 10^8 M_odot$. We conclude that accounting for all types structures in strong-lensing observations is required to improve the accuracy of current and future constraints.