Spin-transport calculations present certain difficulties which are sometimes overlooked when using density-functional theory (DFT) to analyze and predict the behavior of molecular-based devices. We analyze and give examples of some caveats of spintronic calculations using DFT. We first describe how the broken-symmetry problem of DFT can cause serious problems in the evaluation of the spin polarization of electron currents. Next, we signal the low-energy scale of magnetic excitations, which makes them ubiquitous at already rather small biases. The existence of excitations in spin transport has catastrophic consequences in the reliability of the usual transport calculations. Finally, we compare DFT and configuration-interaction calculations of a ferrocene-based double decker that has been heralded as a possible spin-filter, and we cast a word of caution when we show that DFT is qualitatively wrong in the description of both the ground state and the excited states of ferrocene double deckers.