Methods that exploit galaxy clustering to constrain the galaxy-halo relationship, such as the halo occupation distribution (HOD) and conditional luminosity function (CLF), assume halo mass alone suffices to determine a halo's galaxy content. Yet, halo clustering strength depends upon properties other than mass, such as formation time, an effect known as assembly bias. If galaxy characteristics are correlated with these auxiliary halo properties, the basic assumption of standard HOD/CLF methods is violated. We estimate the potential for assembly bias to induce systematic errors in inferred halo occupation statistics. We construct realistic mock galaxy catalogues that exhibit assembly bias as well as companion mock catalogues with identical HODs, but with assembly bias removed. We fit HODs to the galaxy clustering in each catalogue. In the absence of assembly bias, the inferred HODs describe the true HODs well, validating the methodology. However, in all cases with assembly bias, the inferred HODs exhibit significant systematic errors. We conclude that the galaxy-halo relationship inferred from galaxy clustering is subject to significant systematic errors induced by assembly bias. Efforts to model and/or constrain assembly bias should be priorities as assembly bias is a threatening source of systematic error in galaxy evolution and precision cosmology studies.