The pick it multiple times option is normal for certain techs - the warfare tree has at least two of them (refined training and advanced tracking), and the civ tree has refined housing in addition to the one you mentioned.

But I didn't notice that it didn't work.  I'll try to corroborate.

Researching the tech didn't immediately increase my food/turn which it should have if working correctly. I also got 42 food from a farm (precisely that ammount) though I had a granary, and a game hunting thing and was using the +food bonus faction. which sounds about right (rounded up). 15x2 +50%x15 +25%x15

Except it doesn't. I've just confirmed this. The bonus from the food production faction is 50%, gardens were giving 3. They continued to give 3 regardless of how many refined foods I researched.

Because it's advanced farming, not advanced gardening

We have and your report was not reproducible. Testing with one city and only a single farm, while researching intensively and choosing refined farming every time it appeared (8-10 times total each attempt before memory leaks stopped the test) granted an increase of 1-2 food each time, which is exactly as expected for a 10% bonus on a base of 15 food per farm.

The results were the same as Pariden (the food bonus faction) and as another faction. So if you are indeed not getting anything from the research, it must be some special case and we'll need more detail and a savegame to confirm it.