In some instruments (working in reflectance) the reference is exposed to moisture, condensation, dust, volatile chemicals,..., and all these elements contaminate the reference. That is the reason why some instruments tend to protect the reference better in order to avoid these problems.
This is an example: In this case the spectrum of the reference was acquired (32 scans), after that the reference was cleaned carefully.
Let´s subtract the reference before cleaning and after cleaning and look to the patterns, you can get some ideas of the possible contaminants.
Reference subtration spectrum
In some cases are negative spectra similar to some ingredients, fats,, …, which we analyze commonly. It can appear also water vapour signs due to the diference of moisture (water vapour) in the laboratory between the two reference spectra acquisitions (like it seems in this case) .
Of course the scale is amplified quite a lot to see the patterns which can be insignificant for some mayor concentrations, but maybe not for very low concentrations.