This tread has caught my interest since I have noticed (and worried) about the same issue with my VTC5's. Here are my observations:
I have 1 VTC4 purchased in Paris- no discolouration(stronger shrink wrap?)
2 VTC5 purchased in London- 1 has the same issue at the base area like all the others- not over heated-ever!
My charger snaps back and scratchs the shrink wrap with small blemish's and they have the same dark patchs around them.
I believe what you are seeing is just air has gotten into the shrink wrap as previously suggested, in my case where the scratch's were made by the chargers' metal clips and so logically, the darkening around the negative end of the battery is the same effect where the air has (for whatever reason) managed to get under the shrink wrap. No big deal right!!!!
Here is a link to 'Pegasus Academy''s look at 'SONY' batteries and I suggest you look at about 25.00 mins in. Apparently SONY Japan doesn't make our batteries and so they are all fakes made in China!! Check it out
Vaping & Batteries: Things You Should Know - YouTube
If you bought some fake, ' fakes' from ebay, even worse!! There is also a video on the same screen as to how to identify them.
Vape How to Identify Real or Fake 18650 Sony VTC Batteries - YouTube
Hope this helps from a newbie!!