iOS 10.3.2: cookies will return after deletion. How to clean-up?
Also encountered the same problem on my iPhone 6s running iOS 10.3.2. There were some website data that could not be deleted and showed 0 bytes. It is definitely website specific as only a few domains keep popping up while others could be deleted. I tried rebooting my device, clearing safari history and manually deleting each cookie but nothing worked.
What fixed the problem was restoring my iPhone from a recent backup before I've visited the websites. I connected my iPhone to iTunes and clicked the 'Restore iPhone...' button on the device menu. After restoring, I set up my device from backup and all the unwanted website data were gone. Note that this may take a long time.