I've noticed this one a few times. If I change the skillset, and then move a terrain piece or object, and then press Ctrl + Z to undo the move, the skillset resets to what it was before.
I'll keep an eye on this one because to be honest I can't seem to make it happen, it just happens every now and then.
Should be fixed in commit 3ae5ea4.
The source of this issue was that when testing "has the level changed?" for the purpose of writing undo history, skillset changes weren't being taken into account. Thus - a new Undo state wouldn't be saved until another change was made (a different level stat, or a piece moved / added / etc).