I stumbled across an assembly created by someone else where the order of items in the feature tree is unusual:
Somehow, a bunch of components ended up between two component patterns, after the Mates. Furthermore, notice that LocalLPattern7 is a pattern of the component below it (409107). I can roll back the feature tree to before LocalLPattern8, but I cannot roll it back anywhere between the misplaced components. It will roll back to before LocalLPattern7, but misplaced components are still fully accessible and aren't greyed out.
If I drag all the misplaced components to where they would normally be (before the Mates folder), I cannot return then to their original incorrect positions.
I'm curious if anyone else has had this problem and knows if it is a file corruption issue or something else.
There was an SPR 754986 for assembly parts out of order and above the planes/origin in the tree. This was fixed in 2015 SP01, so not sure if it is related or not, but you can look into the workarounds on that SPR in the KB.