That's really interesting. Did you bottle from the keg or did it go into a bottling bucket before bottling?
Bottling bucket. But that has never caused this problem with any other beer when I used to bottle from it before I started kegging a few years ago.
I suspect it is from one of two things, and oxidation is not one of them:
1: hops residue/sediment like oils and particulate plant matter
2: Flaked oats
So hear me out:
I don't think it is from oxidation, because I don't get oxidation flavors. Most of the posters don't (some do mention a funny or off-putting taste, but I think that is coincidental to the color change phenomenon). My bottled NEIPA tastes fine, albeit less hoppy, but that is to be expected.
Since this phenomenon is only observed with NEIPA, I think it is specifically due to one of the ingredients specific to the style. Those ingredients are a massive amount (relative to other beers, including conventional DIPA and IIPA) of unboiled dry hops, and flaked oats, a common ingredient. Yes, flaked oats are used in some other styles, but it's not like you would notice the color change in an oatmeal stout.
I think the observation of the phenomenon in bottles as opposed to kegs is specifically because the bottles allow all that residue still floating in solution to settle out during bottle conditioning and storage. In my case, I know that if I am careful to leave behind the slurry at the bottom of my bottles, it still pours halfway decent (but still not as pretty as from the keg). The reason we don't see it in kegged NEIPA is that the keg is constantly drawing from the bottom, so every time a little of that stuff settles out, we suck it out when we pour a beer and it never gets a chance to accumulate in any large amount like a bottle does. So in essence, the design of the keg prevents the buildup of the precipitated gunk (and since these beers are best enjoyed fresh, we don't let them sit long in the kegs to duplicate bottle aging).
Anyway, a few experiments could confirm or refute my hypothesis (like making a keg of the same NEIPA and letting it sit undisturbed for a month or so and see if it pulls brown), or brewing the same recipe without wheat or oats. I'm not sure I care enough to try either of those, but on my next batch, slated for brewing next weekend, I will try bottling a few bottles from the keg using my Blichmann Beer Gun and see how the bottles end up after sitting a few weeks.