Transition metal dichalcogenides (TMDCs) have attracted significant attention for optoelectronic, photovoltaic and photoelectrochemical applications. The properties of TMDCs are highly dependent on the number of stacked atomic layers, which is usually counted post-fabrication, using a combination of optical methods and atomic force microscopy (AFM) height measurements. Here, we use photoluminescence spectroscopy and three different AFM methods to demonstrate significant discrepancies in height measurements of exfoliated MoSe$_2$ flakes on SiO$_2$ depending on the method used. We highlight that overlooking effects from electrostatic forces, contaminants and surface binding can be misleading when measuring the height of a MoSe$_2$ flake. These factors must be taken into account as a part of the protocol for counting TMDC layers.
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