We report a comprehensive experimental and computational study into low-frequency vibrational dynamics of hydroquinone clathrate during in situ gas loading, in order to monitor replacement of carbon dioxide with methane in its atomic-level pores. We used terahertz time-domain spectroscopy, because terahertz modes are highly sensitive to the identity and structure of enclathrated guest molecules. Through ab initio simulations, we determined that the replacement reaction is not completed. Instead we observed the formation of a heterogeneous material, with methane molecules occupying approximately one-third of available adsorption sites. While the structure of the methane-hydroquinone clathrate system has been previously determined, our observations suggest the reported symmetry is incorrect due to methane molecules weakly interacting with the framework, resulting in dynamic (as opposed to positional) disorder of guests, unlike the related fully ordered carbon dioxide clathrate. This work puts us on the path to quantitatively tracking gas loading in porous materials using terahertz spectroscopy.