Partial skeletons in blocks bins?
Solution 1:
In fact, I think I built the stockpile on top of a previous dump zone (yes, I did build a 11x11 dump zone but I recovered my sanity since, hopefully). This explains why the skeletons were forbidden, because I dumped them in the first place.
That answers point 3 of the questions above. If anybody has clue for 1 & 2 he gets the answer vote :)