you'd think they would use the first-in-first-out method. but it's f**king random. and it's different every f**king time.
It's not random, it's not different every time. It is deterministic. Test it by taking a screenshot of your tree, take the +skill item off and put it back on. Re-allocate the points and do the off/on again. You'll have the same missing points.
First-in-first-out sets up some very frustrating gameplay patterns of reallocating points pre and post boss fights.
I do agree that it should be much more clear as to where the points were removed from.