I should have said I was responding to martinuzz's post and his noticing the fonio bag in the cave wheat stockpile with mixed seeds. The problem of the seeds being stuck in the workshop is something different and I haven't experienced it, and since I thought your second post was an answer to the OP, I branched the thread in reference to the mixed seeds in bags, which I've seen in 40.n.
Because I haven't seen the new problem of seeds being stuck in the workshops, I'm not sure what to think about it, but the "more than one type of seed is stuck in a bag" problem is the same in 47.05 and 50.05 (just tested both versions). It happens because the "store item in bag" seed-bagging code attempts to put a seed into an bag regardless of stockpiles and regardless of the Mix Food setting. The code only asks "is there a bag named for the type of seed or is there an empty bag?".
In 47.05 or 50.05, on a new default embark with no stockpiles, mass dump all bags and seeds and wait until all the bags are empty of seeds. Unforbid one bag and one plump helmet seed, the dwarfs put the seed in the bag and the bag gets a name. Unforbid all the other seeds but only one other bag; the dwarfs take the 4 plump helmet seeds and add them to the named bag, but the remaining 25 seeds, 5 different seed types, are put into the only available empty bag. I like to think this is not a bug because dwarfs are making the smart move by protecting all the seeds instead of leaving them for the vermin... But it probably is a bug because once you are out of empty bags, they don't try to mix seeds anymore.