A little darkening can be normal
Most clear or pale e-liquid drifts toward gold or light amber over the first month after opening. Nothing about that is broken. The liquid is reacting to air and light the same way most clear consumer products do once the seal is off. If your bottle is one or two shades darker than the day you bought it and the flavour still reads correctly on the pull, you are looking at normal aging, not a spoiled bottle.