PLease give us infos about your dye and the kind of glass of your bottle!!
Common glass or borosilicate (lab glass) . Cy name .... Keep your solution cool and in the dark .
A dye like methylene blue salt will ADSORB on the surface of glass. You can see that as follows. Make your stock solution and, after 2 h staying, pour the 100 ml in another bottle. Dry the stock bottle with air and wash it with acetone. Acetone will remain light blue.
A lot of dyes ADSORBS on glass.
The same occurs with quartz cuvettes for UV-Vis spectrometer. You can see the adsorption if you measure the spectrum of the dye (stock sol.) in a clean cuvette and the same solution in a dye coated cuvette. you can see the difference in the spectrum.