This is because you are mixing footnotes and citations. @deustachio_2003 is a text citation: it will be expanded into e.g. "(Deustachio 2003)" or "[1]" depending on your citation style. It is equivalent to the latex \cite{deustachio_2003} command. This is not to be confused with items in the bibliography. The bibliography will automatically be created at the end of the document, so no need to make it yourself using footnotes.
Thanks for the hint Gu. Some further searching turned up the suppress-bibliography option in pandoc so running the same command as before but with an additional parameter of --metadata=suppress-bibliography got me the output I was looking for:
Here is one reference citing the Reactome Project.[^1]
[^1]: P Deustachio, “Pentose Phosphate Pathway,” *Reactome - a Curated
Knowledgebase of Biological Pathways* 5 (March 2003),
<https://doi.org/10.3180/react_1859.1>