A compound can absorb excitation light entering a fluorescent assay or emission light leaving it, reducing the light available for the measured signal. This inner-filter effect depends on absorption at the relevant wavelengths, compound concentration, and optical path length. The resulting readout distortion can produce an apparent positive or negative result depending on how the assay maps fluorescence to biological activity.

Sources:

• https://www.ncbi.nlm.nih.gov/sites/books/NBK343429/