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Over the past decades, investigations of the anomalous low-energy electronic properties of ZrTe$_5$ have reached a wide array of conclusions. An open question is the growth method's impact on the stoichiometry of ZrTe$_5$ samples, especially given the very small density of states near its chemical potential. Here we report on high resolution scanning tunneling microscopy and spectroscopy measurements performed on samples grown via different methods. Using density functional theory calculations, we identify the most prevalent types of atomic defects on the surface of ZrTe$_5$, namely Te vacancies and intercalated Zr atoms. Finally, we precisely quantify their density and outline their role as ionized defects in the anomalous resistivity of this material.