It's happened to me more than once -- hell, it's happened to me a LOT. A darling food or supplement in the ancestral-health world not only didn't help me, it was an outright obstacle to my well-being! Green leafy vegetables, fermented foods, high-fat dairy....
At the top of the list, i reluctantly add fish-sourced omega-3 oil supplements. Yep, the CLO everybody raved about is great for preformed vitamin A and extra D in the wintertime, but i don't believe anymore that "balancing PUFAs" did a lick of good for me. "Contrarywise!" :-)
I discontinued daily CLO use this past summer, and concentrated on getting plenty of sun for my vitamin D intake. My multi already contains it, too, as well as "both kinds" of vitamin A, and i've been making an effort to eat liver at least every fortnight. On a couple of occasions when special restaurant meals have contained something fried, i've come home and taken some CLO, though, to do that balancing thing. In those cases, i've noted but not considered significant that on some occasions my hypothyroid symptoms have flared up badly -- was it mystery ingredients in the restaurant food? Was it excess omega-6? Was it mere coincidence, having to do with stress or allergies? I was suspicious but not convinced.
Well, with the coming of cooler fall weather and less time spent outside in the sun, i decided to start the daily CLO again. Immediately, the low-metabolism hypo symptoms made themselves visible. I find it harder to believe that the extra PUFA, even "healthy" omega-3, is NOT driving this situation.
The FitBit my husband bought me for my birthday even backs up my perception: my resting heartbeat is even better than temperature readings for showing me how my metabolism is responding. Having had to change my principal thyroid-support supplement (fucking FDA...), the dose-adjustment has been much easier. Heart-rate in the sixties, dose is too low; in the upper seventies, perfect. When i supplement with CLO, the HR drops like a stone.
I noted a couple of years ago that a mouse study showed lower thyroid-hormone-receptors on cell walls in the high dietary presence of PUFAs, moderate levels with MUFA predominancy, and the best with SatFats. My own self-experimentation seems to mirror their findings very well. My on-again-off-again use of cod-liver oil confirms it to me.
The only technically-essential fatty acids in the diet are the PUFAs, but they are available in adequate quantities in ANY protein-sufficient paleo-style diet. There are more PUFAs and MUFAs than we need, merely in pastured/grass-finished animal products from eggs to beef. I believe firmly that if we eat good-quality "paleo" protein regularly, we have NO need for supplementation of PUFAs. Trying to increase one's omega-3s? Probably one big hairy mistake.
Your liver will thank you -- it hates PUFAs too, no matter what kind!