To me, this is the curse of the bottom feeder. I struggled with this myself and I am pretty sure I know the cause. This happens when partially vaporized juice gets sucked back into the bottle due to gravity or suction, thus contaminating the juice in the bottle and changing it's flavor profile. I switch between a bunch of different devices so over time the juice in the bottles get contaminated in this way and I need to dump them out, clean the bottle and start from scratch. To get around this I've been filling my bottles less and less.
It would be great if there was a way to prevent the juice from the atty/catch cup contaminating the bottle. Maybe a valve or something that stops backflow in the bottle but allows juice unimpeded from the bottle to the atomizer? I've seen this on other devices (not PVs), but I'm sure something similar could be designed on a smaller scale for a bottom feeder.
I've owned several bottom feeders and I've had this issue with all of them. I do think some juices are more susceptible than others in terms of souring or becoming contaminated. It also depends a lot on your vaping style. Those who vape an entire bottle in one day may not even have this issue, but people who take days to finish a bottle on the other hand, may.