Although EPI phase images are useful (e.g. for Quantitative Susceptibility Mapping), they often contain phase inconsistencies in the slice-select direction which persist and can degrade QSM results. Here, we analysed three EPI datasets in healthy volunteers to characterise these phase inconsistencies and understand whether they occur or interact with interleaved or sequential slice acquisition order. We characterised a ~2Hz cryogen pump artifact in sequential data and slice-to-slice phase jumps in interleaved data. We modified a previously proposed QSM processing pipeline, including 2D (VSHARP) and 3D (PDF) background field removal that removed all through-slice artifacts observed.