Direct detection experiments are still one of the most promising ways to unravel the nature of dark matter. To fully understand how well these experiments constrain the dark matter interactions with the Standard Model particles, all the uncertainties affecting the calculations must be known. It is especially critical now because direct detection experiments recently moved from placing limits only on the two elementary spin independent and spin dependent operators to the complete set of possible operators coupling dark matter and nuclei in non-relativistic theory. In our work, we estimate the effect of nuclear configuration-interaction uncertainties on the exclusion bounds for one of the existing xenon-based experiments for all fifteen operators. We find that for operator number 13 the uncertainty on the coupling between the dark matter and nucleon can reach more than 50% for dark matter masses between 10 and 1000 GeV. In addition, we discuss how quantum computers can help to reduce this uncertainty.